I might have come across a solution for your problem. I have encountered a similar issue on GNOME after installing decibels audio player as flatpak. Afterwards, decibels started each time I was trying to open folders via the GNOME Places extension. I contacted the decibels devs and they pointed me to the Arch wiki
Under 3.3 (Directories are not opened in the file manager), the proposed solution is
xdg-mime default org.gnome.Nautilus.desktop inode/directory
to set nautilus again as the default application for opening directories.
This solved my issue.
I imagine, this could also resolve your issue. Though you might have to replace the nautilus desktop file with the nemo desktop file in the command above, if nemo is your standard file browser.