There has been no secret made about the bad blood between Marvel/Disney and 20th Century Fox over the rights to the X-men characters (as well as the Fantastic Four franchise). With the kind of money made by Deadpool ($322.2m in pure profit for Fox, according to Deadline) at stake, it's not hard to see why there would be, especially in light of the ridiculously small amount that Fox initially paid for the rights to the mutant characters, Wade Wilson included.
According to a transcript from the Industry Focus podcast last year on The Motley Fool , a reading of the court legal filing for the 1993 deal revealed that Fox acquired the X-men live action and animated rights from Marvel for a mere $2.6 million... an amount the two men find laughably less than the cost of buying a house in D.C.
Now, they also note that Marvel still got a percentage of the box office from that initial deal, but as best they could calculate it amounted to only around 2% of worldwide ticket sales on the first X-men film, amounting to roughly $6m in backend compensation.
They don't know if that backend compensation has improved at all over the years, but if it hasn't then Marvel/Disney only earned around $15m off of Fox's Deadpool and the $783m it grossed worldwide, while Fox profited around 124 times their initial investment in the mutant rights for that film alone.