OSMC will only allow me to delete some files but not others via the context menu. The files are shared over SMB. Allow rename/delete is enabled. All permissions for the entire shared drive are all checked as “yes” in Windows.
Are there common causes for this? How do you go about troubleshooting it?
The same way as every other thread in “Help and Support” should be troubleshot:
Need to clean this up
Nope, not from me, wait for the devs to chime in.
There is nothing real obvious in the logs, but I would suggest that you cleanup your sources.xml and remove the reverences to the banned addons 
If the problem is only happening with a few files, my guess is permissions.
I may help to setup a fstab mount to one of the affected shares so we can do some better investigations.
I’m not that well-versed in linux. Will delete these files from Windows and hope the problem goes away for now.
It’s not that difficult to setup fstab plus it has the benefit of better performance.
https://discourse.osmc.tv/t/configuring-fstab-based-samba-share-mounts