When MacGyver finds the holster under the table, it is fastened by screws. But when he goes back with Pete and finds no holster, there are also no screw holes. Since there wasn't time to switch tables, or even turn that one, there should have been holes in the bottom of the table where the screws had been, leaving evidence of the holster's existence.
During Jack's dream of Pete in the coffin, the first shot, he had his right hand atop his left, but in the very next shot, Pete only has his right hand on his stomach.
The reflections in the mirrors do not correspond with the actors' movements; obviously separate camera-takes with choreographed moves and rear-projection screens to look like reflections.
The Vancouver lookout is plainly and dominantly visible in the background during the helicopter arrival, even though many of the cars have California plates and the helicopter has a US registration (N9748C) and it is implied this is set in Los Angeles.
Dalton claims that he does not remember the name of the lovely lady, yet later he addresses her as "Edith".
MacGyver tells Pete that it doesn't look like Jack came to MacGyver's boathouse, yet he says this after only looking downstairs and calling out to Jack, completely avoiding looking upstairs.