I noticed some weird stuff happening with holy wars, I'm not sure if it's intended but when I win a holy war I gain the cities/bishoprics but the county itself stays under the control of the Sheikh that controlled it. Also, I'm unable to declare holy war for some provinces, only weird ducal claims that I don't even possess. I'm using version 2.9b. Also, the vanilla game seems to be working fine in that regard. I can get some screenshots if you need them.
Same thing happened to me, its weird when you go against a duke level pagan/Muslim whose realm is more then his duchy and does not hold the second duchy's title, for example playing as duke of Portucale in my case, I declare a holy war (strangely I found that most other rulers outside the kingdom could declare religious invasion against the Emir of Badajoz but does of the kingdom of Galacia only a holy war) and win it I only get the holding of Badajoz, however to form a kingdom of Portugal I need 2 duke level titles of the Territory and it prevents me like that, and when we go against a Count level pagan/Muslim like you found out, you can't take their main holding, only the baronies associated with that county, but not the county itself.
I myself cannot mod, however I deleted the CB_types text file from the mod and then copy and pasted the vanilla CB_type text file to the mod and I don't know if its done anything wrong but the Religious wars seem to be working once again for me.