There's like 4 different mechanics to explain here:
Different enemy types have different stats (as in, Yetis, Werewolves, and Thugs will always be WAY stronger than normal prisoners, Hobos, and Nerds)
Enemies are color-coded for their strength, I think it goes red > green > gold > white > gray. I think "rare enemies" means the stronger colors.
But ASIDE from their color, enemies can have have unique modifiers based on the adjective that follows their name (i.e "the tough", "the strong", "the virgin", etc). You likely thought a gold enemy felt easier to defeat than a gray because that gray one might have had an adjective that gave him Overblow Protection (it limits how much damage they can take from a single attack, so you couldn't kill him in one attack no matter how much stronger you were, while the gold one was still vulnerable to die in a single attack).
Finally, enemies that have a level next to their name are "Wanted Enemies". Basically any enemy that takes one of Karryn's "first-times" will become a Wanted Enemy (can be an enemy that took a virginity of any kind, or the first one that defeated her in combat or similar things, there's a limited number of Wanted Enemies you can have in a playthrough). Those enemies can randomly show up in any battle and they will level up over time when they are defeated (doesn't make a difference how you defeat them).
If you get a red Wanted Enemy of a strong type, be ready because that motherfucker will be your goddamn nemesis for the rest of that playthrough. On the other hand if you purposefully set a bunch of gray weaklings to be the Wanted Enemies of your playthrough you should have quite the easy time handling them when they show up.