When you talk to an alchemist or enchanter and go into their relevant function, any formula in your inventory that they do not already have will be removed and added to their list (which will be available to other alchemists and enchanters, as well). For some reason in DKS the same thing happens with creature parts trading with any merchant.
I kept a list of the highest level formula and creature parts I found, so I could sell any lesser items before talking to the relevant person (and keep an eye out for ones I needed). With this change in DKS (didn't happen in the original release of D2:ED) it meant a few extra lower level parts got sent to my necromancer when I was trying to sell multiple parts, etc, but with the way the creature building interface is set up that didn't really clutter up the list.
The scroll way past where you are trying to go is annoying, especially since what I wanted to get to (playing the Xbox version) was often near the bottom (newly found books, etc). Once you get the battle tower, though, and can send excess equipment, plants, gems and minerals to the battle tower chest, this becomes much less of a problem. With the alchemy runner able to get any plants you need to make more potions, you can also sell any lower level potions you have to clean up that section of the inventory, and just use the strongest version of each type.
Another selection problem I encountered is that sometimes after using an item in the inventory that empties a slot, the new item highlighted is not necessarily what the game thinks is selected (if it is highlighted but with no arrow marker). Usually in that case I would move up or down to confirm what was selected, but late in the game once accidentally used a quest related potion trying to read the second of three skill books in my inventory (fortunately I had a save immediately before that).
Welcome to the forum.