The text suggests that sort of thing did happen in no small amount:
Then, late in 45 AC, King Maegor entered a new campaign against the rebellious Faith Militant, who had not put down their swords at the new High Septon’s behest. According to an inventory from that time, the next year the king brought back two thousand skulls as trophies from his campaign, which he claimed to be from outlawed Warrior’s Sons and Poor Fellows, though many thought they were more likely the heads of smallfolk who just happened to be in the wrong place at the wrong time.