Plot hole: When Henry and Ellie are cornered in the launch tower during the 'Toppat Recruits' and 'Pardoned Pals' routes, the former goes back in time so that the soldiers that apprehended them were never recruited and therefore the main characters are no longer cornered in the present. However, this should simply cause different people to try to stop them, not an entire removal of the threat.
Factual error: In 'Escaping the Prison', the description for the Opacitator says that it will turn you opaque, allowing you to pass through walls. 2 problems. First, opaque is the opposite of transparent (see through), despite what the description claims. Also, the transparency of objects only affect how much light passes through them, it doesn't affect any other physics (a glass can't go through walls just because it is transparent). Even if the device did make objects opaque, it would not affect any physics or have any effect on Henry.
Suggested correction: The word "opaque" is indeed used incorrectly (there is an achievement you can get called "It's a joke..." by clicking on the word "opaque"), but the Opacitator specifically states, "The more opaque (see through) you get, the easier it will be for you to pass through solid objects." This is just how this specific device works. Not all transparent things can pass through objects, just the person that the Opacitator makes transparent.
Other mistake: In the 'Valiant Hero' ending to 'Completing the Mission', Charles is killed when the space station he is in explodes. Somehow, his headphones survive the explosion that the space station and Charles himself didn't (they are found on his grave at the end).
Suggested correction: Who's to say that the headphones on the grave wasn't a copy or a similar one of the one he was wearing? We never see anyone return to where the ship exploded, so we don't know anything, hence it can not be considered a mistake.
Audio problem: In 'Fleeing the Complex', there is an ending called 'Presumed Dead'. Towards the end of this route, Henry is told that he is the first person to have escaped The Wall. As he is told this however, the person speaking is not moving his mouth.
Suggested correction: Dimitri's mouth was deliberately concealed at that shot, due to him being too small on the screen at that time for the animators to consider adding details. Now, it wouldn't have looked as good if it weren't for his beard.
Then that's also a deliberate mistake.
Continuity mistake: Completing the Mission: At the start of the Toppat Recruits/Pardoned Pals route, Henry and Ellie ride their motorcycle off the cliff and crash into a blue car in the parking lot. There is an overhead shot of all the parked cars in the parking lot, and as the scene continues, some of the cars change direction in which they are facing, and the locations that Henry and Ellie are standing in slightly change depending on the shot.
Continuity mistake: Completing the Mission: In the Special BROvert Ops route, when Henry gets inside the rocket, click "TV Broadcast." Charles starts to lower the TV, and in the next shot, the size of the TV completely changes.
Continuity mistake: Escaping the Prison: At the start, click "File," then click "Cell Door." Henry uses the file to cut out a piece of one of the jail bars. However, the piece he takes out is a lot longer than what he actually cut. Additionally, if you click the JetPack option later on, when Henry flies back into his cell, the cut-out piece has been put back into the door, and it is the proper length that it should have been when Henry took it out.
Other mistake: Escaping the Prison: At the start, click "File," then click "Window." When Henry uses the file to cut out one of the window bars, he climbs through the window, and his head clips through the bars.
Other mistake: Fleeing the Complex: At the start, click "Charge Tackle" and wait for the timer to run out. The fail text says, "Notice that timer? Now you know exactly how much time you have before your terrible reflexes are revealed." This is because in the original versions of the Henry Stickmin games, the timer was only introduced in Fleeing the Complex. However, the timer has been added to all the new versions of the games, so the fail text doesn't make any sense here.
