When Khan in STID said he wanted to "continue the work we were doing before we were banished," Spock (the younger one) replied, "Which, as I understand it, involves the mass genocide of any being you find to be less than superior." Which does conflict with the line in "Space Seed" that there were no massacres under Khan's rule.
I don't see the conflict. Dictators like Khan are obviously going to keep a tight rein on whatever information gets into AND out of their territory. The only reason the records show that there were no massacres under Khan's rule is because he didn't allow word to get out.
Tyrants commit massacres. It's what they do. Especially Augments like Khan - they were literally MADE to do such things.
Besides, anybody who thinks Khan isn't capable of massacres, should ask the families of the crew of Regula 1...