I hate creating new topics but I have the quest to destroy all entrances to the nekkers. However I think I found one and it stated: LMB to destroy the nest. I click LMB and it says: I need to destroy this instead of actually doing it. I casted Aard and igni on it but it doesn't do anything.

Try the grapeshot bomb/trap

If I recall correctly, you need to craft a "Grapeshot" bomb, then when you go up to a nest, Geralt will place the bomb inside. This information should be available in town. Poke around, talk to people and check the quest board near the inn.

I believe you can get the info to make the bombs at the stand in the marketplace, or the bookstore. I can't remember where I bought it exactly.

Then just get the ingredients and make them, then do the LMB prompt.

Also don't forget to make potions and oils as well.

Just one more nest to go. Sadly, I can't find any nest. The guide says it's in the waterfall cave but I can't find it there.

For the cheapskates among us, Geralt CAN learn about monsters by reading, but you can also get the 3 levels of knowledge by repeatedly slaughtering monsters. Hands-on education, as it were.

Wanton slaughter, I knew it was good for something!

I have checked both caves as described in the guide book and found nothing at all.

It's annoying because I only have 1 nest to go. Doing the other killing quest is probably even harder because I've searched every corner of the map and have not found any clue whatsoever.

Ok where is it you get the grapeshot bomb diagram? Can't find it anywhere.

You can get it from Cedric. He's outside the Flotsam in a tree or walking around.

I found one Nekker nest in the forest, and the gapeshot bomb blew it up just fine... but where are the other nests? I checked the enitre cavern behind the waterfall, and the one on the path to the ship (where the guards bodies shot by the elves are) but I can't find any nests in the caves at all!

Yeah the nests are not there at all. I checked it. If you go outside the village into the forest, look for the river. Start following the river. You should find two nests. Apparantly it looks like they sort of respawn because I found them again. Basically they are mostly in the swampy area.

On another note, I'm looking for Endrega cocoons. I found one, once. And recently I found a bunge near each other. Now I managed to kill one queen. I just need to find more cocoons as they don't respawn, at least I think.

I don't know if this is a random thing where they are located, but the pdf guide said you could find them in the caves which is definitely not true for me. One of mine was opposite the ostmurk cave in the forest and 3 more were clustered not far from that further away from the path to the west I think toward the city.