You can click on the worm slot in a tackle box with a stack of worms and use up worms even though the stack on the rod never increases to more than 1

Fixed in e014009

This still happens on 1.18.2

Have you updated Aquaculture 2? :)

yes

I've just tesedt version 2.3.12 for Minecraft 1.18.2 of Aquaculture 2, in a normal CurseForge instance. It works perfectly fine on that version.
My best guess is that you're not actually on that version - you might've updated to an older version perhaps?

Keep in mind it'll still be possible to replace the bait, if the bait attatched to the fishing rod have lost durability or you're swapping to another type of bait.

Can you provide a screenshot of your mods folder?

And when you "swap" the existing bait is deleted? Then I assume what is happening is the bait already in it, though full durability, is being replace with a new one?

I am also on the latest version and that is the behavior I observed.