In the scene that both Zoey and Nate talk, Nate is constantly holding a lizard. However at one point, he can be seen with his hands down with the lizard no where in the shot.
It is never explained why no object disappears when Railtron is created.
When Blaze was trying to recharge his Morph-X Key, the Tronics poured the Morph X in a way where it should have gone down all three tubes, including the two empty ones, as opposed to just flowing into Blaze's Key alone.
When the Yellow Ranger attacks Blaze and kicks him, you can see the wire connected to her in the last few frames of the shot.