I was going to say Thor TDW as well. Maybe Iron Man 2, though that one managed to finish up with the same director all the way through (even though they never had a finished script and the story was basically improvised the entire way through).

As far as “meddling” in general goes, you’ve got Incredible Hulk (the BTS circumstances of which led to Norton being ousted as Banner), Age of Ultron (which led to Whedon abandoning the franchise), the aforementioned Ant-Man (though once Wright left there didn’t seem to be many issues during and after filming), and you could maybe count what happened with Inhumans, too.