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.
Dalton claims that he does not remember the name of the lovely lady, yet later he addresses her as "Edith". However, the 'lovely lady' was an implanted memory while Edith was the person who implanted the memory. Also, on first seeing her, he calls her "lady" as if he doesn't recognize her and only calls her "Edith" once she has spoken the key phrase.
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.