I think i know what happened. This did happen to me -

I joined an alliance but before i did, i applied to join another one.
For a while i could chat with the first clan, but then they just couldnt see me talking or anything, thats when i noticed i was actually in the clan that i applied to. Yet i couldnt see any of them talking. So i ended up having to quit from the current one, costing prestige, and re-apply to the clan i wanted to be in.