Continuity mistake: Before crashing the limo into the fence, there are two bullet holes in the rear windscreen. Afterwards, there are five. Then from an inside shot as they start backing up, there are only two again.
Continuity mistake: Logan tries to give the Professor an injection, who pushes him away and falls over. As he falls back his left sleeve is still rolled up - the shot cuts and it's instantly right down to his wrist.





Answer: It's just a continuity mistake. The blade rips a hole in the shoe, but the hole disappears later on... that's a continuity mistake. It's definitely not a plot hole. A plot hole is more a gap or contradiction in a film's internal logic, or when a film leaves out vital information. (Ex. If a character is established as having a deadly nut allergy, but is eating nuts later on with no ill effect... that would be a plot-hole).
TedStixon