I knew that it's not possible to have same terms (term slugs) under categories and tags, but surprisingly, as I realized today, that's the case with custom taxonomies as well.
So for instance, if my site has a category called
Linux (linux) and I want to create a custom taxonomy term called 'Linux' as well, it'd look something like
Linux (linux-2), i.e. the slugs have to be different.
And if I try to rename the slug back to
linux, I get the error, "The slug 'linux' is already in use by another term".
Is it possible to have the same terms under categories/tags and custom taxonomies (without wreaking havoc)?
How to replicate the issue?
Create 3-5 new posts. Create a new category and tag and assign them to those posts (just for testing purposes).
Save permalink settings.
create two new terms under the custom taxonomy with the same name and slug as the category and tag you created earlier, and assign them to a new post under a custom post type.
Delete the custom taxonomies.
Try recreating them, and you'll now get the error: "The slug 'XXX' is already in use by another term."
Sometimes that'd replicate the issue, sometimes it doesn't.
If you are able to create a category (or tag) and a custom taxonomy with the same name and slug, do it. Then, rename one of them, and you'll notice that both the category (or tag) and the custom taxonomy are renamed!