Its just a normal water jar.

https://ark.fandom.com/wiki/Water_Jar

What I mean is the engram inside the Beer Barrel for the Beer Jar is marked in yellow and says it needs to be learned, and every time a cycle of Beer Liquid finishes it just vanishes rather than turning into a Beer Jar (with water jars in the inventory)

It also strangely lists TWO different Beer Jar engrams in the station, and only one of which seems to even see the Water Jars in there.

See these screenshots
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2785754739
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2785754784

A year or two ago the vanilla game changed how engrams appear in crafting structures. They now show unlearned recipes as yellow in such structures. I believe this can be toggled off. To be clear, you do not need to learn anything here.

Beer liquid should automatically disappear and fill a water jar when created.

If you see unusual behaviour... Ensure your stacking mod is correctly higher in the load order and then pickup/replace the beer barrel.

Yeah I know I can turn it off, but I like seeing progress. Strange that they are yellow here though and not in other stations. In any case I'm assuming the double engram showing up is the real issue but I have no idea why.

I am not using any stacking mods, if by stacking you mean mods that modify item stacks. (to the best of my knowledge).

Saddle Emporium
Immersive Taming
Item Finder
Breedable Griffon Mod
Auto Engrams!
Low Steal Icthy
Super Structures
Homing Pigeon
Classic Flyers
Vacuum Sorter
Kanga Storage
No Cryo Cooldown