I was playing a vanilla world and started placing wheat seeds in crop sticks and it never used the seeds up as long as i placed them in crops sticks. After some it seems the bug happens to any seed that wasn't run through the seed analyzer.
The mods i was using were:
Agricraft
Botania
Baubles
EnderIO
Fast Leaf Decay
Faster Ladder Climbing
Inventory Tweaks
Iron Chests
JEI (Just Enough Items)
Mouse Tweaks
Mystical Agriculture
Mystical Additions
Refined Storage
Thermal Expansion
Thermal Foundation
VeinMiner
Waila
I was using Forge version: forge-12.18.3.2316
I had no config changes aswell

Were you in creative mode, by chance? The mod checks for that and won't consume seeds and stuff in that case. Also there's a problem when you attempt to harvest mature plants, which will let you collect more seeds than normal.

That said, a18 has a few crash-causing bugs, so you might want to switch back to a17 if you're not ready for sudden crashes.

I was in survival, and was just planting unanalyzed vanilla wheat seeds in crop sticks and it never used the seeds, I spawned in other seeds (unanalyzed) using JEI and planted them in crop sticks (still in survival) and it didn't use one of them. It seems once you analyze them the exploit stops working.
And yes i downgraded to a17 after crashing multiple times while walking over crop sticks (should i make another thread for this aswell?)

Hmm, interesting details. Thank you! Were the other spawned seeds vanilla or from AgriCraft? And did you still see this behavior on a17 too?

Meanwhile, I think I found the cause: TileEntityCrop.java, plantSeed / onApplySeeds
In the "Experimental API Refactoring" commit, seed planting was rewritten, and the new method doesn't update the stack anymore. I looked over the chain of events for when a crop gets right clicked, and I don't see another new place that tries to do it either. So maybe this is just an oversight? RlonRyan will be able to answer best, he wrote the update.

Edit/PS: so what I said about creative mode isn't true anymore, oops!

For the crashes, it depends on what the error reported is, and search for the name of the error using the filter box on the Issues page. I would guess that it was an AbstractMethodError.

Yup. You are right @CodesCubesAndCrashes. I seem to have broken the consuming code with that commit. I probably didn't notice since I test mainly in creative mode...

I'm on vacation for now but hopefully when I get back on Wednesday I can resume work on AgriCraft. I think I want to overhaul the stack helper class as so it has a method to handle stack size changes so that I don't have to copy the code everywhere and forget about it in places.

@RlonRyan Nice, enjoy the vacation!

And yup, same mistake for me.