I’ve been experiencing problems like this myself. I did some Radar spelunking and it seems to be a known issue (r. 28479011). It should be relatively easy to work around: just undo what the capability does, that is, remove the MapKit framework from your project. The capability will still says its on, but it won’t have any effect on your built app.
Alternatively, you could revert the change via your source code control system.
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