I've found that if I set my default Python version to a Python 3 virtual environment, it breaks some system tools on my Fedora system (probably just because my virtual env doesn't have the necessary libraries installed, though I haven't tried to install them to test). Specifically gnome-tweak-tools, but probably others that are built with Python. Sort of a funny quirk.
That's not me saying "don't use virtual environments", just be aware you'll probably need to switch back for some system tools.
This is strong evidence that something is set up wrong in your system. pyenv doesn’t change /usr/bin/python. If an app is using your PATH to find python it is going to break.
The apps in question use a shebang of `#!/usr/bin/env python3`. I believe it is working as designed. This is a Fedora system, which switched to Python 3 a couple of revisions back. But, I would assume this would affect any system that has utilities that use that shebang.
Edit: Out of curiosity, I grepped for other system utilities that might have this quirk, and it seems like nearly all Python utilities call /usr/bin/python3 directly, but ten of them (on my system) use `env`. That might be a bug worth filing with the Fedora folks. I can't imagine they want it to act this way when a custom Python is installed. Though it's been that way for at least a couple of releases.
That's not me saying "don't use virtual environments", just be aware you'll probably need to switch back for some system tools.