Your challenge filter only comes into play with challenges. So, if you have your maximum number of games set at 16, and you are already playing 16, no-one can challenge you.
It doesn't mean you can only play 16 games - you can issue as many challenges as you want and play, ladder, tournament and clan games. Time controls for clan games are agreed between the leaders and your clan leader can put you down for as many games as he/she wants. If you don't want any more clan games, you need to make yourself unavailable for clan challenges via your settings.
General challenge settings only apply to casual / friendly games. Tournament, clan, ladder games can still add to your list.
To block clan games go to MySettings > MyClanSettings and untick the boxes for the clans that are listed there. It's a courtesy to PM your clan leader and advise him why you're doing it and how long you're likely to be blocked. Clan leaders have the option to boot you out if you remain unavailable for too long, because they need active players and are limited to a total of 20.