On the Road - S2-E1
Revealing mistake: As Cassidy, Tulip, and Jesse are trying to outrun a police car, another cop car enters the road in front of theirs with tires squealing. There are tire skid marks On the Road before the cop car enters, indicating previous takes of the same stunt.
Fence + Suitcase + Americium-241 - S3-E12
Revealing mistake: When MacGyver cuts the green wire under the bomb, the wire is not tied up at both ends. (00:25:45)