I hope I can answer this with an answer I posted a while back here Chromium "Show in Folder" opens in text editor
(That would make this a duplicate so it might get closed ;) )
In ~/.local/share/applications/mimeapps.list
there is a list of files to be opend by an application. Have a look with more ~/.local/share/applications/mimeapps.list
and check if you can find something weird here. You can use vi or gedit to edit this file.
But there is also a command mimeopen that allows you to alter what program should open what file (and that updates the file I mentioned before). It will 'guess' what would be the most logical option based on the file you feed it.
mimeopen -d /home/{your_name}/Documents
Please choose a default application for files of type inode/directory
1) Open Folder (nautilus-folder-handler)
2) Other...
mimeopen -d \[Mazui\]_Ore_No_Imouto_-_14_\[SD\]\[7EA51F50\].mkv
Please choose a default application for files of type video/x-matroska
1) Enqueue in SMPlayer (smplayer_enqueue)
2) Movie Player (totem)
3) SMPlayer (smplayer)
4) Banshee (banshee)
5) VLC media player (vlc)
6) Other...
Same works for a torrent file and any other file.
Maybe you already know this but if you can not get to command line use control-alt-f1 and log in with your sudo user account and password. control-alt-f7 gets you back to your desktop.