Basically, if there are Too many mobs spawned in the world, the vanilla mobs will not spawn.
Even if you set the limits in Incontrol.
if you lower the mob amount, they will spawn, thing is, they should spawn regardless.

Example, i set Incontrol to spawn 10 zombies. NO MORE, NO LESS.
If there are too many other mobs, the zombies will NOT spawn. (or spawn very few).
This happens regardless of if you use "remove": "minecraft:zombie" before the command or not.
IT happens regardless of if you set "allow" in Spawn.json

It seams to be effected by the vanilla mob cap.

This issue does not happen on modded mobs, or mobs outside their natural habitat (AKA blaze in overworld)

Well that's hard to avoid. In Control just fires whenever the vanilla subsystem tries to spawn a mob. If vanilla itself imposes restrictions on top of that then that's not something In Control can avoid

would it be possible to allow incontrol to change the individual mob caps?
I know Mocreatures has the ability, but i rather use incontrol since it gives more control.

This is possible but requires some thinking first (internal note: check out LivingPackSizeEvent)