Ah, there it is. I didn't know that. That answers my biggest question. I guess the effects crew prioritized Jungle Book much more than XM:A, since I've heard nothing but great praise on the CGI quality in that film (I personally haven't seen it yet). That, or they were given more time/CGI to budget ratio was better allocated/all of the above.Chances are they hadn't planned anything out untill the time of writing the story treatment.
As for any problems I am willing to bet there were no issues beyond the effects guys working on jungle book at the same time as apocalypse.
Apocalypse was much more busier then DOFP, that's pretty much all it is, they wanted to do everything with it so it was a bigger balancing act to pull off.