Editor inserting bootstrap css and we don’t know why

Without checking your install it’s a bit of a guessing game, but I’d say your TinyMCE editor has a bootstrap plugin installed (there are several). Perhaps the developer tried to remove it, but only removed the buttons in the editor. Any case, it might be active without you noticing, with the plugin’s jquery interfering with WordPress, leading to erratic behaviour.

Also, the plugin may not be on your own server, but loaded from a cdn. Have you checked the editor page html for strings like ‘bootstrap’?

Completely different option: some plugin is messing with your content by adding itself to the save_post hook. But this looks less likely to me, because I can’t see why a plugin would do this.