I figured it out. Opened AE went to preferences. Clicked on General. Went to the bottom and and clicked "Reveal Preferences in Finder". Selected te folder that that file was in and went to permissions and made it read/write on all the selection and it worked.
Hope this might help someone else. I had no clue where the preferences were located at in the finder and didn't know about that button.
As you found out, but for the benefit of everyone else...
When you upgrade a Mac OS (as opposed to installing the new version fresh), Mac OS will _often_ set permissions of folders and files incorrectly.
You'll see this problem in programs like After Effects in the form of error messages saying that a file can't be written, overwritten, or renamed.
To fix this in the case of After Effects, go to the preferences folder and set the _entire_ preferences folder ( /Library/Preferences/Adobe/After Effects/12.0/ ) and all of its contents to be writable, not read-only.