Just had 2 cyssts removed from my head, there was a blood clot behind one of them and the gp said that this should disperse on its own. Is this true?

Probably. It is not clear if you mean intracranial (inside the head) cysts or cysts on your scalp, but either way it is not uncommon to have some bleeding after surgery. A hematoma (blood clot) may develop at sites of bleeding. In general, if the hematoma is not causing pressure on important structures and as long as there is no active bleeding, the body will reabsorb the clot over time.