what mods are you using ? maybe Survival+ ?

no, mainly some building mods. nothing that affects dinos except the classic flyers

classic flyers could be the problem if they rename the character_BP_Wyvern

all it does is undo the nerf

Downloaded the mod to see what it contains, it has the same character BP's as vanilla dino's, which to my understanding is adding extra wyverns to the spawn. As technically it is a separate dino from the vanilla ones, is it not? I could be wrong, but I believe this is how it works.

So likely the cause is classic flyers. To test, remove classic flyers from your server/SP mod list and load it back up, check if there is still over spawning. (Probably best to dino wipe, but if you remove the mod it should remove the modded dino's.)

Wyvern_Character_BP_Base
Wyvern_Character_BP_Fire
Wyvern_Character_BP_Lightning
Wyvern_Character_BP_Poison
Wyvern_Character_BP_ZombieBaseClassic
Wyvern_Character_BP_ZombieFire
Wyvern_Character_BP_ZombieLightning
Wyvern_Character_BP_ZombiePoison

It is highly unlikely that the problem is caused by ShigoIslands. I test this map daily and have yet to have a problem. Over spawning only happens when you add new dino mods to the mix.

Wyverns were overspawning on the Scorched Earth map even before our server added any mods. We've noticed that wyverns usually despawn as they fly into the cliffs, and have a tendency to despawn after a period of time unless they are in a chunk potentially loaded by players. I'm betting that the devs knew they had 1) a spawn problem, and 2) a potential game balance issue.

It might have nothing to do with either the map or classic flyers.