Shortly after Capt. Woodward debriefs Jackson and Armstrong in his office, Armstrong emerges from the room in front of Jackson, despite them leaving in the reverse order.
When Joe and Jackson jump off the cliff into the awaiting motor boat, the fall far from each other, and with a lot of momentum, yet when they are shown landing they are almost touching, and easily drop into the craft with a soft landing.
When inspector Singh and his assistant leaves Capt. Woodward's office after the talk about Taylor's death, Singh puts his hat on. On the next shot, he can be seen putting his hat on again.
In the beach brawl scene, when Jackson leaves the boat and goes looking for Joe, he has no shoes on. After he finds Joe and both are running for the boat, Jackson has black gym shoes on, they can be seen while running and before jumping for the boat.
Joe throws a sword at a ninja who shoots arrows at him from atop a boulder, causing him to fall off and hit the ground. However, the ninja falls in a way that would have him landing on his head, yet when the camera cuts to a shot of the landing, he lands on his back, making the shot uneven.
There are numerous errors in procedure during the meeting with the CO in the beginning of the movie. The army salutes its superior officers even indoors. Also instead of going to attention they go at ease. Even then there's a mistake as Joe goes at ease with his hand in front of him instead of behind.
Joe and Curtis obviously borrowed their Dress Blue uniforms from Staff Sergeant McDonald. Provided they also borrowed his ribbon set as well, both Joe and Curtis are wearing different ribbons from one another. Furthermore, the only row of ribbons that do match between the two of them is the bottom row, however they are in a different order which would be unlikely even if the two sets of uniforms actually belonged to them as ribbons and metals are arranged by precedence.
Near the start when Jackson and Armstrong leaves Capt. Woodward's office, it can be clearly seen that Guy Pringle, Michael Dudikoff's stunt double, plays Dudikoff's role for a brief moment.
Throughout the film, people are slashed with swords and killed, yet their clothing remains intact.
The bombs that Professor Sandborne detonates in the lab supposedly destroy the entire lab, but it's clearly obvious from their explosions that they only flash brightly for a moment, and are pretty much contained to their respective cells. Their flames don't even touch Sandborne or the Lion.
Shortly before the ninja is dragged by the pickup truck driven by Joe, he throws a grappling hook towards the rear of the vehicle. The rope clearly falls short off the truck, yet in the next shot it lands precisely and grabs its back corner.
During the bar fight while rescuing Alicia, Charlie gets thrown against the bar where a woman smashes a bottle over his head. She is impatient for her cue and reaches for her bottle twice before she is supposed to. Finally on the third time she smashes the bottle on his head.
Throughout the series, Joe is shown to have well-honed ninja senses, borne from his intense training in Ninjutsu. For example, in the original film, he is able to fight Jackson with a bucket over his head and sense his movements perfectly, and shown to sense which drum has a ninja in it when in the middle of a sword fight in the warehouse. In this film, he is shown to sense, without looking, as Tojo Ken breaks from their pre-fight ritual to take a cheap shot at him. Yet when alone with Taylor at the Blind Beggar, inexplicably, it is Taylor-an untrained, regular "civilian"-who hears an ever-so-quiet noise outside his door (which turn out to be ninjas there to assassinate him) and not Joe.
The film's secondary title, "The Confrontation," makes no sense, in that there is no central confrontation that takes place in the plot. There are dozens of confrontations as the plot plays out, but none that stand out as "special" in any way, or even acknowledged as anything more than fights that come up as they do.
At the window, just before he's assassinated, Taylor goes to the window after hearing a noise. As he begins to open the curtains, a shadow of each of his assassins is visible through the curtain, approaching to kill him and, indeed, doing so seconds later, yet even though he is a trained ninja-with cultivated senses and quick thinking that he displays multiple times throughout the franchise-and even though he is standing right behind Taylor, watching, Joe does not warn him or yank him away from the source of danger, etc. He stays completely silent and just watches the fatal incident unfold - to say nothing of not hearing the same sound Taylor hears, even though his senses are developed and Taylor's are not.
Joe and Jackson narrowly escape hordes of ninjas who are trying to kill or kidnap them on Mangrove Island, managing to flee after dumping off a high cliff and into the marines' boat, after which the ninjas are shown watching their boat escape to safety. The shot of the boat escaping to safety features Joe and Jackson sitting with the marines, with everyone sitting in their seats leisurely, and Taylor even sitting in the back, with his feet up, as if nothing just happened, when in reality, the marines have just rescued their fellow soldiers after one of them went missing, and watched them jump off of a high cliff with a horde of ninjas in tow. They'd most likely be crowded together, asking them if they were okay, asking them what happened, etc., and not just lounging back in their seats, like normal.
During the beach brawl, Joe takes on several ninjas, with him slashing the blade off of one of their swords. Inexplicably, that ninja does not factor into the fight any further, even though he's standing right behind Joe, is able to attack him otherwise, and is free to do so as Joe is busy fending off multiple other ninjas.
In Tojo Ken's final moments, he is heard exhaling in pain, yet his mouth is closed at the same time.
The scene where Tojo Ken kills a bunch of Ninja during the demonstration makes no sense. Not only is it wasteful, it also shows that the so called super soldiers are easily killed by just one man.
When Professor Sanborn reviews his research, and what they have been able to create with their work, he describes the ninja army in several impressive ways, yet all of them are easily and openly refutable throughout the film, as if not given the slightest attention to maintain congruence. For example, he describes the ninjas as being engineered to be "cunning, intelligent, and devious," yet they are comically inefficient at fighting, as evidenced by the beach fight, where hordes of them are easily dispatched by both Jackson (a non-ninja) and Joe. One of them is even shown to climb on top of a truck, only to get bashed in the face a moment later, comically falling right back off. Sanborn also claims "the ninjas feel no pain," yet Joe leaves one screaming in pain (in front of Alicia's house) after breaking his leg, and another one screaming after lighting him on fire. Sanborn also claims the ninjas' muscles and sinews are replaced with "the strongest high-tensile steel known to man," yet Joe breaks the leg of one of them with ease, Jackson breaks the arm of one of them on the beach, and Joe breaks the neck of one of them on the beach. Sanborn describes the ninjas as "stronger than a ten-ton crane," yet one of them has great difficulty simply climbing up a rope as he's dragged from a truck. Finally, Sanborn claims the ninjas are "faster than an Olympic athlete," yet Joe and Jackson outrun them to escape them on the beach.
When Professor Sanborn reviews his research, and what they have been able to create with their work, he describes the ninja army in several impressive ways, yet all of them are easily and openly refutable throughout the film, as if not given the slightest attention to maintain congruence. For example, he describes the ninjas as being engineered to be "cunning, intelligent, and devious," yet they are comically inefficient at fighting, as evidenced by the beach fight, where hordes of them are easily dispatched by both Jackson (a non-ninja) and Joe. One of them is even shown to climb on top of a truck, only to get bashed in the face a moment later, comically falling right back off. Sanborn also claims the ninjas feel no pain," yet Joe leaves one screaming in pain (in front of Alicia's house) after breaking his leg, and another one screaming after lighting him on fire. Sanborn also claims the ninjas' muscles and sinews are replaced with "the strongest high-tensile steel known to man," yet Joe breaks the leg of one of them with ease, Jackson breaks the arm of one of them on the beach, and Joe breaks the beck of one of them on the beach. Sanborn describes the ninjas as "stronger than a ten-ton crane," yet one of them has great difficulty simply climbing up a rope as he's dragged from a truck. Finally, Sanborn claims the ninjas are "faster than an Olympic athlete," yet Joe and Jackson outrun them to escape them on the beach.
At one point Joe and Curtis are wearing the US Army Class A service uniform. They wear identical ribbons, and both of them wear their ribbons in the incorrect order. The correct order would be the Army Achievement Medal by itself, centered on the second row, with the bottom row consisting of the National Defense Service Medal, the Army Service Ribbon, and the US Army Overseas Service Ribbon, left to right (as you face it) in that order.
Both Joe and Curtis wear a ribbon-only version of the National Defense Service Medal. Assuming the movie takes places in the same year it was released (1987), and assuming that Joe and Curtis enlisted around the time of the previous film (1985, very likely considering their low rank), neither of them is eligible for the National Defense Service Medal. The National Defense Service Medal is only awarded to US military service members on active duty during a time of war. Since eligibility for the medal ended with the conclusion of the Vietnam War in 1974, and the next period of eligibility would not be until 1990 with the start of the Persian Gulf War, neither Joe nor Curtis would be eligible for the medal.