In the end, when Wells is sitting in front of Stagg, he takes off his glasses. The camera angle changes to the back of Wells, facing Stagg, You can see Wells has his glasses back on. When the camera changes to face Wells again, he's holding his glasses in his hand.
When talking with Joe, Barry states that he can run a mile in 3 seconds. That would be equivalent to averaging 1200mph or mach 1.56, which is much faster than Barry can run at this point in time.
When Iris says "Something out there is saving people," the shot changes and her mouth isn't moving along with the last part of the line.
They explain how the bad guy can clone himself, but they never explain how he can clone his clothes and shoes (but not a gun).