1. Timing Discrepancies
In the original X-Men film trilogy, the character of Charles Xavier is introduced as an elderly wheelchair-bound man who maintains a rivalry with his onetime friend Magneto. Details are never explicitly given about when Xavier became paralysed or when he and Magneto became adversaries. A scene at the beginning of X-Men: The Last Stand shows him visiting Jean Grey twenty years prior to the start of the film (presumably 1986), able to walk and accompanied by a friendly Magneto, however, indicating that both events happened some time after that year. X-Men: First Class, explicitly showcases both events despite being set in 1962. If the film was still meant to be a reboot (as it was originally envisioned), then this divergence would be irrelevant, but now it is being linked to a series where Xavier was still mobile and friendly with Magneto twenty four years later, it is a somewhat glaring storyline inconsistency (and means that by the time of the original X-Men film, the two have been opposing each other for nearly forty years).
And there you have it, eight discrepancies, both major and minor, that slightly hinder the overall plot of the X-Men film franchise in a variety of ways. I should point out that I have enjoyed each film in the franchise (barring Origins), and that this article should not come across as a rant, rather as a piece that merely illustrates the problems that can arise when film series attempt to branch together a host of sequels and prequels. Any discussions are welcomed in the comments section.