Which issues are you talking about?
Complicated to explain - I'm gonna try to boiler plate it down because walls of text stink. LOL
Marvel worked out an arrangement with Fox and Sony - they rented the licensing rights of Xmen to Fox, Spider-Man to Sony. The problem is length of time for these agreements.
Marvel was in a state of bankruptcy at the time of these arrangements. The movie licensing allowed Marvel to stay in business. As long as Fox and Sony made new movies on a regular basis, the contract is good.
Disney bought Marvel.
Marvel has their own movie studio
(Marvel Studios) and is able to produce their properties with success. Guardians, Avengers, Thor, etc.
It is believed Marvel want their rights back of the Xmen and Spider-Man.
This has lead to the belief that Marvel is not promoting the Xmen properly because they don't want to support Fox. Marvel wants their licensing back but due to their agreement, they don't have access to the Xmen in the movie realm. Any character deemed in the Xmen world is off limits to Marvel Studios. Thus Marvel's supportive approach to properties like Inhumans, Avengers and all of their other stuff that they have complete control over in all forms.
If Disney buys Fox - the licensing for the Xmen will go back to Marvel as Fox would become a subsidiary of the Disney/Marvel brand.
There is a whole thread on the opinion of all of this at CBR. It's called "The Complex".
Edit: Anyone else have more details or if I've misstated something or what have you, please contribute.