It appears there is an actual bug from this. While I was able to get the files do show up they will throw an error about not having permission to view them when a user tries to open them. Viewing permissions on the file itself shows that it still is inheriting permissions from its previous parent library (which it is no longer associated with). Clicking the "Break Inheritance" button throws a return code 0 error.
The only way I was able to fix this was to delete the files and re-upload them so they would gain the correct inheritance for the library.