so, I was wondering what guilds dont work together for a single playthrough? I know you can only join one great house, And the fighters guild kills the thief's guild people, and the mages guild kills the telvanni councilors. But what other guild interfer with eachother? I was planning to make a battlemage and wanted to join the Fighters guild and Mages Guild, Was thinking of Telvanni aswell till I realized they dont work together with the killing of eachothers members..

Both of them work together well except for those two you mention, but they are optional and that too right at the end. So no problem. Also you have the choice of killing both of them who give orders.
But you should know that by doing code book quest first for Fighters guild doesnt allow you to join Thieves guild afterwards.Just join Thieves guild before that.

In my last playthrough, I joined both Mages guild and Telvanni and became Archmage and Archmargister with no problem.

PS: May be the only quirk of joining Mages guild and Telvanni is probably while RPing.