During the talk with Lincoln over the view screen, old footage is reused. Notice that in shots facing the view screen, Checkov is replaced by another crewman and Sulu is wearing a season one uniform.
About 25 minutes in, there is another reversed shot as the good guys discuss what to do, right before Colonel Green comes over. Notice that Shatner turns left to talk to Lincoln who is on his right and that the Starfleet insignia is on his right side, not left.
The close-up on Lincoln as Surak screams is taken from his speech about being a woodsman from a few moments earlier.
Barry Atwater who played Surak has noticeable difficulty giving the Vulcan "Live long and prosper sign", and he still doesn't get it right: he holds his thumb against his index finger instead of separate.
During the fight with Colonel Green, Kirk's pants split up the back, but in subsequent shots they're fine.