the-witcher-3
I'm sure I have the recipe for the Samum Bomb (to destroy monster nests). But after using two of my own crafted bombs, I see 0/2 in my inventory.
If I try to recreate such bombs with the matching ingredients, I get the hint: "You already have this item". That's not really true .-) Actually I have 0 of 2 of this bombs and can not destroy a third nest.
How can I replenish my stock of Samum Bombs?
The Medidation Menu is on the Far Right of the Menu.
There are two menus.
One is a menu where you can save game, load game, exit, etc..
The other is where you have your World Map, Inventory and the Meditation Menu. It's on the Far Right of this Menu.
You can see it here in this image:
You can then select the span of time (You can see the current time you're on and select When you want the meditation to end.) and it will fast-forward to that chosen time healing you in the process.
If you're playing in higher difficulties (Any above "Story and Sword") you will not heal during meditation but the game will always warn you about that.
You can destroy Monster Nests just like in Witcher 2. Crafting or Buying Bombs and using them on the Nests.
In the Witcher 3 it works the same way you have to blow up the nests but with some new twists. Before you would go to the nest and press a button to drop the bomb.
Now in the Witcher 3 you can throw a bomb towards the nest or use a destructive sign at it to destroy it.
"look around the chamber until you spot the two smoking mounds lying either side of the pit. As instructed, use either bombs or one of your destructive spells to obliterate them" - Quote from Guide
The specific bomb to destroy nests in the Witcher 2 was the Grapeshot Bomb.
EDIT:
Ghouls Nests and Nekker Nests can only be destroyed with bombs. Get a Samum Bomb or Grapeshot Bomb (Most Common) and go to the Nest and will ask you to press a button to drop de bomb just like in Witcher 2. Some nests can be destroyed by using the bomb and Igni and some only with Igni.
Endrega nests (Eggs) can be destroyed using Igni and so can rats nests.
If you need to replenish your bombs just meditate with Strong Alcohol like Alcohest and they will refill along with your potions.
Best Answer
You replenish bombs the same way you replenish your witcher potions - by meditating. You'll use 1 of your strong alcohols, but it will replenish everything.
A list of strong spirits can be found in this question