I've only ever seen two parts of git that could arguably be called unintuitive, and they both got fixes:

• git reset seems to do 2 unrelated things for some people. Nowadays git restore exists.
• the inconsistent difference between a..b and a...b commit ranges in various commands. This is admittedly obscure enough that I would have to look up the manual half the time anyway.
• I suppose we could call the fact that man git foo didn't used to work unintuitive I guess.

The tooling to integrate git submodule into normal tree operations could be improved though. But nowadays there's git subtree for all the people who want to do it wrong but easily.

The only reason people complain so much about git is that it's the only VCS that's actually widely used anymore. All the others have worse problems, but there's nobody left to complain about them.