Yes, because they are special:
. is the current directory where you are in. The OS will not allow you to remove the directory where you currently are. The
.. directory is the directory above that one. These are not real files and cannot be the reason for your troubles. Try this in your top-level app directory:
find . -name ".*"
Then delete those files. Files which begin with a period are not normally shown when by tools that list files.
I told you: that is not a real file and cannot be removed. A sure way to verify this to recreate the directory structure somewhere else and manually copy each file this leaving behind any "undeletable" problematic files.