In the second story, when Leela starts killing her friends, when she kicks the Professor into the hole of man-eating anteaters, the Professor was holding a plate. When he falls in, he is not holding it. When Hermes shows Leela the video will of Leela kicking the Professor in, the plate isn't even there.
In the second story, "What if Fry never came to the future", the Fry Hole contains Bender, Zoidberg, Farnsworth, and Leela; however, if Fry didn't go to the future, Bender and Leela would have never met Farnsworth and Zoidberg (at least not soon enough to be in the Hole). The only person that should have been in that Hole is Leela or that guy who says "Welcome to the world of tomorrow!" in that weird voice since they worked at the Cryogenics lab at the time Fry was unfrozen.
During Frys story intro, Scruffys hat and mustache swap colors back and forth from grey and brown.
When Giant Zoidberg cuts off Giant Bender's feet, Bender is standing in grass. When he stumbles back in the next shot, he's in a barren field of dirt and rubble.
Giant Bender is 500ft tall and the Empire state building 1200ft tall. So when he falls on to it there is no way it can pierce him in the middle of his back.