Is it possible that if you use Blender too much things get messed up?

Once you have a somewhat reliable workflow for what you are trying to achieve, things are going to get a lot simpler. After that, it will likely get a lot easier to adjust your workflow, try other things out and what not.
One of the simplest ways to overcome that initial burden is by asking questions. Even though everyone has their own workflows, there are plenty of people who had similar experiences who have a way better technical understanding of Blender than you do. Use that!

Judging from this thread Mixamo to Blender, sometimes it works, sometimes fails... Why? you simply don’t have a clean workflow established yet. At least this one isn’t a Blender issue.