When Bruce Banner transforms into the Hulk for the first time (during the "Wolverine" segment) the hole in his left pant leg mends itself.
During Wolverine's fight with Team X, his claws keep changing from being sheathed to being extended.
Sif's sword changes frequently from having a slight bevel to it, to being curved like a Japanese katana and taking the appearance of a broadsword.
The blood often seems to disappear on a characters body, like when Wolverine stabs Hulk in the back, there is blood. Then in the next shot, there is no blood.
When Omega Red strangles Wolverine with his tentacles, his arms alternate between being up in the wide shots and lowered in his closeups.
Loki refers to Thor as his Step-Brother. Thor is his adoptive brother.