^Well, there was the whole Prof-X-walking-in-Origins thing. But yeah, I suppose it's FC which contradicts Origins and TLS, as they both had an older Xavier walking.
It's not so much continuity errors - and you can have continuity errors in any sequel or prequel - which bother me as the need they apparently felt in Origins to wipe the slate (and Logan's mind) at the end and try to ensure that all fitted in with the movies made earlier but set later. At least in a post-TLS sequel, you can shake the box up a bit.