Well, I can’t read their mind so I can’t tell if silently deactivating COVID apps for the second time was another honest mistake (although I would hope they would try to prevent making the same mistake twice!) or not.
For closed libraries, I think you mean Magic Earth, the included (proprietary) GPS app in /e/OS. Well, included until recently, IIRC they removed it. They genuinely seemed to believe the developers may Open Source the app at some point in the future though, from what I can tell. Otherwise /e/OS doesn’t use anything proprietary (aside from drivers, but that is just required to make Android run on phones)