If you have custom/modified WMO, I can't help you, try what dahaga wrote.
If you are using blizzlike WMO:
1) Make sure you don't have 2 WMOs spawned at same coords (duplicated object, made by 2 presses of ctrl+v, import from txt or just bug of saving ADTs).
2) Don't spawn M2s inside of WMOs with indoor spaces (especially buildings and caves). Use only gameobjects and doodad sets for spawning interiors, otherwise follow dahaga's advice.
3) Make sure you have flattened terrain under building and that you have holes on right places. Objects can flicker even when you are running on floor which is too near to the ground texture, so also make sure your building isn't too "deep" in the terrain texture.
4) In cellars and caves make sure that you have terrain texture everywhere enough high above the ceiling.