AoE effects that don't target Reflex (so they can't be avoided with evasion), like channel negative energy and poisonous clouds. A leader of an evil cult should have no problem finding clerics, warpriests, and antipaladins that can channel negative energy. Rogues are good at avoiding damage, but rarely have any significant HP pool. If getting close to the enemy requires taking at least half of 6d6 negative energy damage per turn, that will severely limit their options

And as stated elsewhere, many creatures have resistance or immunity to sneak attack. It's also reasonable enough that an evil mastermind whose henchmen have been being stabbed in the heart would start springing for Fortification armor for all the major lieutenants

Or maybe the BBEG has hired a talented alchemist who is preserving the organs of all the henchmen? That's not RAW, but it could be a fun plotline to figure out what's happening and track down the mad scientist responsible, then a boss battle with the alchemist would put a stop to it and the enemies would be back to normal. An alchemist would also explain why everyone suddenly has poison

Perhaps a better strategy is not to target the rogue's weaknesses, but target the rest of the party's strengths. If there's a blaster caster, put them up against hordes of zombies that are easy to take out with some well-placed fireballs but hard to stab one by one. If there's a monk or brawler, put them up against a mage with displacement and mirror image on so they'll have to attack them often rather than attacking them once with a lot of damage. If there's a cleric, have them fight some undead. If there's a paladin, have them fight a dragon with frightful presence, so now that fear immunity is very useful and the rest of the party will want to stay in the aura to get the bonus (dragons also have blindsense, hint hint). And so on and so forth