Yes, some bosses have special powers or passive bonuses that make them tougher. Some examples include: Can't be dodged, Can't be crit, Can't be blocked, Super dodge, Counter-attacker, and more.

Its up to you to determine the best strategy to beat that specific boss. For example, if a boss can't be crit, then you can trade out crit runes for defensive runes. If a boss can't be dodged, you can trade out your dodge runes for offensive runes or different defensive runes. Its up to you to determine the best strategy.

Every boss is definitely not the same.