Actually my bad completely. Please lock this topic.

i have no idea if you have played the previous Witcher games but a Grapeshot bomb was the bomb of choice for destroying nests.
You will have the crafting recipe for Grapeshot bomb as it's part of an early quest in Witcher 3 the quest also explains what the Grapeshot bomb can be used for.

I have played previous games. Grapeshot was required to destroy nekker nests. This time it is somun, and it is for both ghoul and nekker nests. Apparently rats nests are different, or it is a bug.

EDIT:

Apparently they can be destroyed with signs... excuse me while i retreat in shame...