A few days ago, Bleeding Cool reported on an agreement between Marvel and Disney for Disney Publishing to have all publishing rights regarding the movie/comic Big Hero 6 produced by Disney and loosely based on the Marvel comic.
It didn't answer why exactly Disney weren't publishing the Big Hero 6 manga in the US, letting Yen Press have the rights.
Well, after publication, I was contacted by a number of people at both Marvel and Disney wanting to have their say.
There was some contradiction, but there were some very common threads. That specifically before this agreement between Disney Animation, Disney Publishing and Marvel, there was considerable conflict.
Initially, Marvel wanted the movie aimed at an older audience and Disney refused. Marvel then refused to publish comics to support the movie. So Disney told Marvel they would publish comics themselves (not the manga, but original comics by US creators). It was then that Marvel went, and I quote, "apeshit".
Cooler heads prevailed and an agreement was drawn up. That Marvel wouldn't get involved with Big Hero 6 at all, the marketing the publishing and the like, but Disney Publishing were not allowed to publish Big Hero 6 comics in the US. Hence the Yen Press deal for the Disney Japanese Big Hero 6 manga.
An uneasy accord was arranged, and everyone was then singing from the same songsheet. Until Marvel EIC Axel Alonso's comments on CBR, "We wanted the Disney folks to be able to create their own unique style and story, unencumbered by those older stories" and then certain folk at Disney Animation kicked off again… as Marvel clearly didn't want that.
[UPDATE: More responses denying any kind of war and stressing cooperation throughout…]