Clownfish Mating Pair?
 

So I've had 3 percula clownfish for about a year and a half now and just recenty saw the smallest of the three kinda on his own all the time. The other two just follow eachother around. They arent agressive to the other one but he looks lonely and hes moving slower on his own. Also the biggest one is fluttering his tail in the sand ALOT like hes practicing to make a nest. Will i have to get rid of the small one? Or could they not even be mating?

Sounds like the bigger two are flirting, but probably not breeding yet. Trios of Perculas don't usually work...you will probably have to find a home for the third one.

What Myka said. Get the little one out before it is too late.