The problem is that dot files (._000atl.rpy) which are metadata files that appear (normally if you access the files from a non mac network share iirc) were in the directory. To fix this I had to:
dot_clean [App Bundle File]
xattr -cr [App Bundle File]
If you do these steps before you zip the application it should avoid this problem. Simply moving the file (and I know why you suggested it) isn't enough