Berne Vampire Clan/Tribunal Temple Conflicting Quest
If you are in the Tribunal Temple and want to be a Berne Vampire, you MUST NOT complete the last Temple quest in Molag Mar. This quest involves wiping out the whole Berne Clan HQ, and will make it impossible to join them.

Telvanni/Berne Vampire Clan Conflict
When, you are building your Telvanni stronghold, you wil be forced to retrieve the book "Secrets of the Dwenmer Animunculi" from Berne HQ. If you have the Amulet of Shadows(found on Invisible guy, after you kill him, north of Gnisis, by a pond), you can easily sneek by all the vampires, and steal the book off of the table right next to Raxle Berne himself.

Thieves Guild/Fighters Guild Conflicting Quests
There is a way to complete both factions.
1. You MUST join the Thieves Guild first. If you join the Fighters guild first you will NOT be able to join the Thieves Guild.
2. Complete the Thieves Guild entirely.
3. Buy the Codebook from the Imperial Woman, in the South Wall Corner Club in Balmora.
4. Complete most of Fighters Guild and SIDE W/ PERCIOUS(in Ald-Ruhn)
5. Complete the Fighters Guild.