
Proof coins often become toned inside the cellophane envelopes. If it becomes ugly it will hurt the resale value of the set, although sometimes attractive toning occurs which is a plus. Your nickel looks like it has developed a yellowish toning spot above Monticello but we need better, focused photos to comment further.
It's unlikely you have rotated die coins in your set. The coins should all show the same orientation of the obverse and reverse, in which the back side is exactly upside down compared to the front. If any coin is otherwise oriented it could be a significant error.