Are you keeping your project and the Crashlytics framework in Dropbox? I've noticed that Dropbox changes/resets the permissions set.
Try pausing Dropbox sync and then set the permissions of Crashlytics.framework/run
to 755.
UPDATE:
chmod 755 run
only worked temporarily for me.
As Hemal Shah wrote in his answer, I also had to tell git to make run
executable. You can do so by calling git update-index --chmod=+x run
and committing that. (via this answer).
After having moved my project and the Crashlytics framework out of Dropbox, and doing this, there were no further issues with it.