I think you're mainly referring to me here - I was in LuFredd when this clan league started, so I was presented in their roster.
Despite getting into another clan before the clan league ended, I still represent LuFredd for this season; just like Nogals still represents Mhunters.
Also, I don't think there's any problem with being in a different clan than the one you're playing for in CL.
Just to make an example, Miyagi plays for Apex even if he's in Masters clan (https://www.warlight.net/MultiPlayer/Tournament?ID=15709
), but he's not the only one of course
I know seeing teammates with different clan logos may be a little confusing, but as long as they were presented in the roster they're breaking no rule.