Emptying a bottle of Iron Wine by crafting it by itself in the 2x2 crafting grid and clicking to pick up the result gives an empty bottle in hand, but also leaves an empty bottle in the crafting grid that can be taken.

This is reproducible for me but not 100% reproducible. I don't know what the x factor is.

Do you have Binnie's mod installed?

No, no forestry or Binnie's.
Mod list:
ae2stuff-0.7.0.4-mc1.12.2.jar
AkashicTome-1.2-10.jar
AppleCore-mc1.12.2-3.1.0.jar
AppleSkin-mc1.12-1.0.9.jar
appliedenergistics2-rv5-stable-7.jar
astralsorcery-1.12.2-1.8.5.jar
AutoRegLib-1.3-15.jar
base-1.12.2-3.5.0.jar
Baubles-1.12-1.5.2.jar
bdlib-1.14.3.12-mc1.12.2.jar
BetterBoilers-1.1.1.jar
BetterBuildersWands-1.12-0.11.1.245+69d0d70.jar
BetterFps-1.4.8.jar
Biome_Bundle-1.12.2-v6.1.jar
bonsaitrees-1.0.1-b56.jar
Botania r1.10-353.jar
Chameleon-1.12-4.1.3.jar
ChestTransporter-1.12-2.8.7.jar
Chisel-MC1.12-0.1.1.26.jar
chiselsandbits-14.12.jar
CodeChickenLib-1.12.2-3.1.5.331-universal.jar
CoFHCore-1.12.2-4.3.10.4-universal.jar
CoFHWorld-1.12.2-1.1.1.12-universal.jar
ContentTweaker-1.12.2-4.3.0.jar
Controlling-3.0.5.jar
CookingForBlockheads_1.12.1-6.3.17.jar
CraftTweaker2-1.12-4.0.12.jar
CTM-MC1.12-0.2.3.9.jar
deepresonance-1.12-1.6.0.jar
diethopper-1.1.jar
Earthworks-1.12-1.3.6.jar
ElecCore-1.12.2-1.8.434.jar
Ender Ore-1.12.2-b1.jar
EnderStorage-1.12.2-2.4.2.126-universal.jar
environmentalcreepers-1.12.1-1.2.1.jar
Exchangers-1.12.2-2.6.2.jar
ExtraCells-1.12.2-2.5.11a48.jar
extrautils2-1.12-1.7.2.jar
fairylights-2.1.2-1.12.x.jar
FastLeafDecay-v14.jar
Forgelin-1.6.0.jar
ImmersiveEngineering-0.12-76-core.jar
ImmersiveEngineering-0.12-76.jar
immersivepetroleum-1.12.2-1.1.7.jar
immersivetech-1.12-1.3.4.jar
industrialforegoing-1.12.2-1.7.1-116.jar
InventoryTweaks-1.63.jar
IronBackpacks-1.12.2-3.0.5-6.jar
ironchest-1.12.2-7.0.34.820.jar
IvToolkit-1.3.3-1.12.jar
jei_1.12.2-4.8.5.143.jar
journeymap-1.12.2-5.5.2.jar
JustEnoughResources-1.12.2-0.8.6.33.jar
LootTweaker-1.12-0.0.6.5.jar
malisisblocks-1.12.2-6.1.0.jar
malisiscore-1.12.2-6.4.0.jar
malisisdoors-1.12.2-7.3.0.jar
malisisswitches-1.12.2-5.1.0.jar
Mantle-1.12-1.3.1.21.jar
mcjtylib-1.12-2.6.3.jar
MCMultiPart-2.4.1.jar
modtweaker-4.0.6b.jar
moreoverlays-1.13-mc1.12.1.jar
Morph-o-Tool-1.2-16.jar
Morpheus-1.12-3.3.2.jar
MouseTweaks-2.8-mc1.12.1.jar
MTLib-3.0.1.jar
natura-1.12.2-4.3.2.42.jar
NetherPortalFix_1.12.1-5.3.13.jar
NotEnoughScaffold-1.12.2-1.5b.jar
Notes-1.12-1.1.1.jar
OpenTerrainGenerator-1.12.2 - v4.jar
OTG-Core.jar
Pam's HarvestCraft 1.12.2m.jar
PortableCrafting-1.12.2-1.0.2.jar
Quark-r1.4-122.jar
RecurrentComplex-1.4.7.jar
RedstoneArsenal-1.12.2-2.3.10.4-universal.jar
RedstoneFlux-1.12-2.0.1.2-universal.jar
rflux-1.12-0.2.0.jar
rftools-1.12-7.27.jar
RoguelikeDungeons-1.12.2-1.8.0.jar
rustic-0.4.8.jar
SpiceOfLife-mc1.12-1.3.11.jar
StorageDrawers-1.12.2-5.3.4.jar
TConstruct-1.12.2-2.9.0.55.jar
tesla-core-lib-1.12-1.0.12.jar
theoneprobe-1.12-1.4.19.jar
ThermalDynamics-1.12.2-2.3.10.4-universal.jar
ThermalExpansion-1.12.2-5.3.10.15-universal.jar
ThermalFoundation-1.12.2-2.3.10.6-universal.jar
TrashSlot_1.12.1-8.4.6.jar
twilightforest-1.12.2-3.6.324-universal.jar
VeinMiner-1.12-0.38.1.639+134fb1e.jar

Just reproduced this again after a server restart. From an initial stack of 3 bottles I am now using 2 for brewing and have an additional 7 in a mini chest. Of course, when I went to record it, it wouldn't repro.

Finally captured it in action. https://imgur.com/eFjDEfV

Might be another mod conflict, or maybe it's just a bug in Rustic that I totally forgot about. I'll look into this for the next release.

Hm. This doesn't seem to be a mod conflict, and I can reproduce this, but for me the extra bottle disappears as soon as I click it. Seems like a client/server desync. Not entirely sure how to fix this.

Oh, actually, I think I fixed it. It's hard to be 100% certain, but I'm pretty sure it's fixed. I plan on releasing an update with this fix and more within a day or two.

The update was just released.