Other mistake: When Rube is searching the hard-copy (paper) archives, the young man with him opens the last box and pulls out an old "Wanted" poster with Rube's face on it. He tells Rube "This guy looks just like you." Since season 1, episode 1, we've known that Grim Reapers don't look like they did when they were alive (i.e., Millie/Un-George). Yet somehow, Rube has not changed since his life/death.
Other mistake: In the scene where Raphael and Michelangelo report from their ceiling vantage point, we see a hallway full of Foot ninjas. Strangely, we can see a brief shot of an Earth Protection Force trooper walking peacefully among amongst the Foot even though they are hostile to them. (00:07:50)Daniel4646