The issue is the following:

I have a testing environment with bunch of integration tests running one after the other. They are using MongoDB, and using the same database and collections.

I only have some unique indices there and there, there are no regular indices.

Between fixtures I reset the database just by calling collection.deleteMany({}) in each collection.

In 4.4.3 it was fine, but after 5.0.3 upgrade I noticed a serious performance degradation. After some investigation, I found that every test case took a slightly more time to run than the previous one, and it slowly added up, and to the end I can see test cases took 2x more time to finish than did with 4.4.3.

What I ended up with, when I drop and recreate indices between fixtures, I get the same performance as it was with 4.4.3.

So I suspect that somehow unique indices of deleted entries are not getting deleted automatically causing performance degradation for live data.