This happens when a zipped patch does not contain a directory and then the files, but instead the patch files are all in the root of the .zip archive. For example patch.zip/main.pd instead of patch.zip/patch/main.pd.
It’s super annoying, and the solution is to find the last patch you installed, open the .zip on your computer, and then delete all the matching files from your Organelle. Then go leave a comment on Patchstorage telling the creator that they need to repackage the patch.
It should be fairly easy for the Organelle’s patch install script handle this problem by locating main.pd and treating that as the root of the patch. Hopefully it will be updated in the future. Anyway, until then, I hope this helps with your Organelle journey! 