If browser or some another appication opens file or something else in wrong application, it can fix the next way:

An example if browser opens some else application than filemanager.

Query about current mimetype:

xdg-mime query default inode/directory

Test about current mimetype:

XDG_CURRENT_DESKTOP='X-Generic' xdg-open ~

Change default mimetype (if wanting caja):

xdg-mime default caja.desktop inode/directory

… and again

Query about current mimetype:

xdg-mime query default inode/directory

Test about current mimetype:

XDG_CURRENT_DESKTOP='X-Generic' xdg-open ~

Used mimetypes can be found from

$HOME/.config/mimeapps.list

xdg-open $HOME/.config/mimeapps.list