In one scene, Tim says something about "the Greninjas being set free." The plural form of a Pokemon is the same as the singular form, so he should have said "the Greninja were being set free." Other characters in the movie get this right.
While in the bar, Tim attempts to pretend to be talking with someone on his phone so that people won't think he's crazy for talking to Pikachu whom only he can understand. At one point he sets his phone down to directly talk to Pikachu. In the next shot, the phone has completely disappeared from the counter.
From the top floor of Howard Clifford's building, after Tim Goodman removes the transmitter from Clifford's head inducing Mewtwo and Pikachu's fall, Tim miraculously finds himself downstairs in a matter of seconds.