When Dodd first comes after Leonard and chases him, his red SUV blocks in Leonard's Jaguar from behind. However, in the next chronological scene (when Leonard gets back to his car and drives away), Dodd's SUV is no longer blocking him in.
When Natalie kisses Leonard goodbye, her lips are not cut, though they are before and after.
When Leonard burns Catherine's hairbrush in the fire, you can
see that Catherine's book is also burning next to it before Leonard has put it into the fire.
In the black/white parts Leonard is staying in room 21 (as seen on the key). In one of the shots he looks out the window and we see the door to room 304. In the clip it is at the same height as the room Leonard is looking out of, but when he moves into that room he has to go down the stairs to get to the reception and in doing so passes room 21.
The serial number on Teddy's polaroid picture is 12847001532 at the beginning of the movie but 07946087152 when Leonard writes on it later on.
The vial of insulin used by Sammy has the lettering "C-II" on the label, indicating that a medication is a controlled substance (schedule II). C-II medications are those with high abuse potential and include narcotics like morphine and fentanyl. Insulin is not a controlled substance, much less a C-II, and would not have this designation.
The Jaguar XK8 has antilock brakes and would not have managed the entertainingly screeching skid as it stopped outside the tattoo parlor. Only the rear wheels are locked and clearly the handbrake was used to make an amusing noise. No matter how it was achieved, it was not a natural stop and there is no evidence to suggest that Leonard is a stunt driver who might habitually stop like that.
When Natalie shows Leonard the picture of herself with Jimmy, she is smiling (in addition to Jimmy having a mustache). Later, when he gets out of bed and views it again, she is no longer smiling, and Jimmy's mustache is gone. Finally, in the close-up of Leonard writing the note on the back of the Polaroid he took of her, the picture has reverted to its original state. This is probably deliberate to make us feel we have Leonard's condition.
When Leonard is sitting in his pick-up writing down Teddy's license number, he writes "FACT 6" without checking how many other facts there are first.
This the whole point the film is making, that Leonard's memory is both reliable and unreliable. Are the number of facts he has tattooed on himself something buried in his long-term memory, or something he forgets in the short term.
Sammy Jankis is reported as having "possible damage in the hippocampus, nothing conclusive" but the CT scan of his brain shown at the time is grossly abnormal. It shows a large left sided subdural haematoma (bleed) with significant mass effect. It is very likely that a patient with such a scan would be seriously unwell. However, since Sammy is a fabrication of Leonard's memory, it is highly likely that this brain scan is in fact a scan of his own brain, fitting the description of bleeding.
Natalie's handwriting is different in each of its appearances. The writing on the Ferdy's Bar coaster switches between print and cursive, and the invitation to the City Grill is in another kind of print. However, this could be another demonstration of the instability of Leonard's memory.
Leonard can keep his memories for only a few minutes throughout the movie, but the "memory reset" somehow takes much longer to occur during the final reveal scene.
It has been explained that Leonard can keep his memories as long as he can focus or not stress then he eventually lets go of them.
When Teddy asks Leonard to roll up his car window near the beginning of the film, the top of the intact window is briefly visible, pushing the loose shards of glass, before retracting.
When Leonard discovers the bullets in the pickup, the primers are obviously used and would not fire.
Teddy's head is pulsating when lying on the floor after having being shot.
In the close-up shot of Natalie's head on Lenny's torso, you can hear Lenny talk with the same voice whether he is breathing in or out.
When Leonard and Teddy are in the diner, Teddy says "What about John G? You think he's still here?" When the scene cuts back to Leonard, the line "You think he's still here?" is heard, but Teddy's mouth isn't moving.
When Dodd pulls his red vehicle into view after Leonard turns
off the road to see what he was harassing him about, the camera crew is reflected on the side as the truck moves from the right side of the frame to the left.
Leonard goes to the Discount Inn, and the manager takes him to room 303; when Leonard realizes that it is not his room and the manager admits to also renting him room 304 because business was slow, Leonard calls the manager Burt. In that particular entire sequence, Burt has on no name tag, nor does he mention his name to Leonard.
During the confrontation between Leonard and Teddy after Leonard has killed Jimmy, Leonard mentions the $200,000 in Jimmy's car. However, at this point he has already forgotten about killing Jimmy, so he should also have forgotten about the money as Teddy doesn't mention it.
While the fact that Leonard wrote "do not trust her" in a different style of writing, so that he knows to be suspicious of it, is supposed to be a detail deliberately added, Leonard also followed notes written by Natalie more than once, even before he had a Polaroid of her, or any reason to trust her.
Natalie apparently rides home from the bar with Leonard, yet her car is already home.
After fleeing Dodd, while driving to the hotel, Leonard is reading the description that Natalie wrote down for him. You hear him 'thinking' what she's written down. He 'says' that Dodd is staying at the Mountcrest Inn, yet it is written as the Monterest Inn.
In the Jaguar Teddy gives Leonard the address of the Discount Inn. Teddy met Leonard at this motel earlier and therefore knows that he is already staying there. Leonard did not check out when they left and should therefore have both a picture and the key to room 21 in his possession.
After Leonard has locked Dodd in the closet, he calls Teddy for help without any good reason to trust Teddy (and many reasons to mistrust him).
When Natalie wakes up with Leonard in her bed, she is surprised at Leonard's tattoos even though she saw them just last night.