I strained my hamstring about 3 months ago, my hamstring never had the chance to fully heal , still causes pain when i sprint , what could this be?

Get evaluated: Hamstring strains can be chronically problematic if not treated properly. I would follow up with an orthopedist to make sure you did not have anything more than a strain. If the injury is severe enough you can get partial tearing or even a full rupture of the tendon from its insertion site. If it is just a strain then you might need some therapy. Either way see an orthopedist since its been 3 mo.