Go to the bottom of this page a table with all the factions and their attitude towards others.

http://www.uesp.net/wiki/Morrowind:Facti ...

Some conflicts, how to join thieves after they found Fighters Code Book, and there are some that you kill the members of another clan, which may already be in demand (for example, are asked to kill, when in government and government Telvanni Mages Guild), but you can avoid them.