It's a weird issue that showed up when 2.7.2 came out. Along with adding cults for all of the religions, including unreformed pagans and heretics, it made recruiting for cults easier, because beforehand it was stiflingly difficult to recruit people for your cult and it was practically impossible to do anything with it. (I remember my attempts at a Zoroastrian run kept getting screwed up by my heir refusing to convert.) The issue now is that it spreads crazy fast and is almost impossible to prevent. They recruit everybody they can--courtiers, minor vassals, family members, anybody--and it spreads like wildfire from there. The AI joins cults for the hell of it, and Hunt Apostates works way too slowly to root out everyone. It's compounded by the fact that banishing these characters or otherwise allowing them to go to other realms just causes them to turn the cult international.
If it were up to me, I'd make it difficult or impossible for anybody to convert anybody who's not important (a councillor, a count-tier or higher ruler, or a member of your direct family) and make it so you need something particularly convincing to convert a ruler (like the ruler having Cynical, preexisting religious sympathies, or a friendship with the cultist.) Additionally, I'd significantly reduce the chance of characters falsely converting when their conversion is demanded by their liege, make Christian and Dharman rulers always refuse to join cults for non-heretical religions in the same group, and perhaps require AI rulers to have something like Zealous, a good religious education, or a high Learning stat to found a cult in the first place.
Barring (or perhaps in addition to) that, I'd add an ironman-compatible option to make it so only the player can found a cult, similarly to how by default only the player can become immortal, satanspawn, or wolf's blood, or how you can turn off the AI taking the Seduction or Intrigue foci.