I'm sorry to be the bearer of bad news but unfortunately you won't be eligible for rewards during this CvC. 

Per the CvC rule page: 

i

Unfortunately that leaves you ineligible for rewards since you left and came back mid CvC. Again, sorry about that. 

I don't want to try to press the join-team-button to confirm it, but from the things the OP telled, you immediately change the clan by pressing it once. Maybe there should be an "are-you-sure?"-button to solve this problem?

That's exactly my issue, I was never shown a prompt that asked if i was sure i wanted to leave or something along the line saying that if you leave you wont be elegible for the rewards or something. Also how are players allowed to join a clan when already being a part of a clan?

That was my 2nd time participating on a clan tournament and I have only been playing for a little after a month. Also the fact that the game itself doesn't have the ability to recognize that i was alrady a part of the clan with participation already stablished when i re-joined shows an issue with the game.

I understand joining a brand new clan mid section but re-joining my original clan and loosing all the progress made up until the point i left is just bad programming.