Even though I solved the issue with what I said before, I was still getting error sometimes.
I found the issue that python3-nautilus still had some leftovers.
Debugging it was easy, just run nautilus on the terminal and it's gonna show some warning such as:
_ImportError: could not import gobject (error was: 'No module named gi.*gobject’)*
(nautilus:5395): Nautilus-Python-WARNING: pygobject initialization failed*
(nautilus:5395): Nautilus-Python-WARNING: nautilus_python_init_python failed*
This initialization was causing the issues. Removing everything about this solved my issue.
Hope it helps @Abdulhalim @fegauthier