Eh, it's no worse than the original series 'continuity'. Attack of the 50ft Irma - Turtles apparently see the transport module for the first time. Same goes for April Fools and The Old Switcheroo where they all react too seeing it for the first time, or the lava flooding the tube.
Personally, I think the second batch of episodes is a leap higher than the first. We've got good ones like The Journal in the first, but in the second half, almost all are good. Timing is Everything, the last Bishop episode, etc. Even the animation seems too have been improved a bit, although the turtles still have that cheap look about them with the straight lined designs...