Biggest Plot Hole? S-P-O-I-L-E-R-S (of course)
For me, it was that the cubes ended up in their original position in two days.
If the number of permutations was on the order of 17 thousand, and each move stayed in place for about 5 minutes, as in the film... that's about 60 days!
It also puts the kibosh on Quentin (the fascist) finding them so fast. He had no skills to calculate his way to their cubette.
What was it for you?