Well it really depends on which show/movie your looking at , Im Twilight its because the vampiros kill people and the lobos are the protectors but in vampire diares its because there both uncontrollable things so really it depends but form all the fiction things i have read over the years its más of just a mortal enemy type thing that there naturaly born to kill each other
The hombres lobo came into existence as protectors of their tribe. Then a pair of vampiros attacked the tribe and another neighbouring tribe. Those vampiros were the most dangerous enemies the lobos had ever fought. They've been natural enemies ever since.