I dunno about mutants having separate contracts if their first appearance was outside of an X-Comic, but I can think of several cases where Marvel Studios might be able to claim overlap:
*Beast --- was a major member of the Avengers for several decades. In terms of film, Fox seems pretty clear that they intend to hold on to him, though, and I've never heard Feige & Company express any interest in acquiring him.
*Cloak & Dagger --- A few years ago, Marvel Studios were developing a TV show based on these two mutants. The show vanished into vaporware, but its existence (even on paper) muddles the copyright issues even further, since Marvel's live TV rights are allegedly a lot broader than the feature film franchises.
*Similarly, the Six Pack were in TV development for awhile, I guess as a kiddie show. All those younguns are muties.
*Namor --- he's the odd man out for right now, belonging to Universal, and they don't seem to have any plans developing a standalone movie about him at all. Chances are, at some point, Marvel Studios and Fox will start a bidding war for the rights. Not sure when those expire at Universal.
*Typhoid Mary --- technically, she's a mutant. And she appeared in Elektra, which was still a Fox movie, so there was no discrepancy there when she appeared. Nowadays, Kevin Feige has confirmed that Elektra, Kingpin and several other characters who are vital to the Daredevil mythos belong to Marvel Studios now (or are at least shared). I'd say there's a good chance that Mary would fall under the Daredevil/Elektra banner.