Other mistake: At the beginning of the film when April sees the foot clan braking into the shipping container, it is pouring with rain, yet her hair miraculously remains dry all the way through.
Other mistake: When Donatello is deactivating the countdown, the last 5 seconds on the countdown is shown and the voice on the computer is heard counting down each second. Every one second the voice on the computer counts down is actually two seconds passing in real time.
Other mistake: When the turtles blood is being drained, all four tubes have blood running through them, even though there are only three turtles in the containment boxes.
Other mistake: When April views the tapes of her dad she's around 10-11 in them, but Sachs looks the same as he does in the film and this took place in the past perhaps 15 years, before current times.
Suggested correction: That isn't a plot hole. Vernon assumed April was the person calling him and was correct. People do this all the time in real life.
BaconIsMyBFF