We only had a problem with wyvern spawns when we had Classic Flyers installed, and it broke both griffin and wyvern spawns. CF is integrated into Extinction Core so you could get rid of it and do a dino wipe to reset your spawns.

If you're not using CF, it should just be "wyvern"

Here's a guide for ya! https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=739263442

Does ec have its own unique tag for vanilla dinos? Because I have a stego infestation on my server lol

Extinction Core does have an unique tag for a large majority of dinos. They usually have _Core_C at the end. Such as the following

Raptor_Character_BP_Core_C

I'm not sure about your stego situation, but I suspect that the wyvern overspawn issue has to do with Classic Flyer mod, assuming you have installed that. Classic flyer actually messes up EC, and it's also not needed as all flyers in the game are replaced with EC's version of stronger and faster flyers...and the ability to lvl up speed too.

I'd probably check other mods that might spawn other dinos as well, and check to see if the stegos are EC or not (that's the hard part).

We have moved on to new map without extinction now but why was it only wyverns and not all flyers