Further testing I did, which is easily recreated:
1. Perform virgin WP install (6.0.1), php 7.4
2. Add 2 plugins to this WP: Ultimate Member and Admin Menu Editor.
3. Create a new user & set to Pending Review status so that UM will add the bubble notice.
4. Activate Admin Menu Editor. Bubble remains.
5. Open Admin Menu Editor UI and hide any Users submenu item. Bubble vanishes!
6. Unhide submenu item. Bubble still gone.
7. Use “Load default menu” and save. Bubble still gone.
8. Clear all caches, cookies, the works. Bubble still gone.
9. Deactivate Admin Menu Editor. Bubble returns!
10. Reactivate Admin Menu Editor. Bubble vanishes.
11. Deactivate and DELETE Admin Menu Editor. Install and activate Admin Menu Editor. Bubble remains.
12. Hide Users parent item, then unhide. Bubble still gone.
13. Visit site, clear caches, return to admin. Bubble still gone.
As you can see, the problem arises when a menu item containing a bubble notice is tampered with via Admin Menu Editor, and it stays a problem until Admin Menu Editor is deactived (deleted and reinstalled, if user wants to change menu items other than those with bubbles while retaining the bubbles).
This behavior occurs even when the submenu item being hidden is not the top/first item.
Your plugin is doing things with the database that isn’t playing nice with other plugins and the offender(s) is/are getting removed upon deleting your plugin.
It could be a UM-exclusive thing, but I suspect this is a universal incompatibility. I have yet to verify that, though, since UM is the only plugin I use at the moment that adds a bubble notice.