Description of the issue:

Bottling machine has a chance of consuming liquids yet not turning the input item into the pre-set output item. This issue kept showing up when I was playing survival mode. At first everything works well but after some time of game play there's a chance that this will happen.

It is worth noting that this issue will go away for a little while after rebooting the game, but come back after some time in the game.

I know the script isn't wrong because the recipe worked, I suspect it has something to do with the ram and lag build up over time in game play. Also once this issue occurs, the recipe will be broken forever until fixing it by rebooting the game.

I haven't tested the issue with other bottling recopies that came with the mod, but here's the crafttweaker scripts I wrote:
mods.immersiveengineering.BottlingMachine.addRecipe(machinemod:fuelcan*1, machinemod:fuelcan:1000*1, liquid:gasoline*1000);

mods.immersiveengineering.BottlingMachine.addRecipe(cfm:item_soap*1, rustic:tallow*1, liquid:oliveoil*1000);

I've post an issue at the crafttweaker bug report post as well, I'm not sure this issue is on them because this sort of recipe script worked flawlessly in previous IE versions from a modpack I played last year.

Crashlog:

The bug didn't crashed the game, no crashlog was generated.

Versions & Modlist

Minecraft: 1.12.2
Forge: 14.23.5.2837
ImmersiveEngineering: 0.12-89
Mod List:
https://pastebin.com/474RqmAQ

Can you reproduce this with a recipes from base IE?

Can not confirm with IE's own recipes, but I'm experiencing the same issue, but I can only complete one crafting operation before the thing breaks.

I'm experiencing the same issue with custom CraftTweaker recipes.

I am having the same problem on the same build of the mod, but I am on forge 14.23.5.2823. The bug happens anytime I try to fill a second glass bottle after filling a first one. Both the second glass bottle and its fluid is destroyed. Afterwards I have to reload the world or any more bottles will not be filled and fluid will be lost. This only happens when attempting to fill a bottle with a fluid. When fluid is put into Jerrycan or bucket, no fluid or container is lost.

As a side note the only shared mods between OP and me are Gravestone, Jei, CodeChicken mods, NoMoreRecipeConflicts, and obviously immersive engineering.

A Quick Update:

Using Forge: 14.23.5.2823, Immersive Engineering 0.12-91, and CTM 0.3.3.22 I was able to replicate the bug once more. However I was able to determine the bug most often occurs when you immediately store the Bottling Machine's output directly in a chest, and you immediately remove the bottle from the chest. (Such as if a player bottles potions for immediate use)

Leaving the bottles in the chest for a period of time decreases the chance of the glitch occurring. (Like a player bottling potions for later) Interestingly, having the bottles drop into the world does not trigger the glitch. Also having the bottle go down a conveyor into a chest does not trigger the glitch.

Unfortunately I have no logs, as none were generated.

Setup that produced glitch the most:
Front
Back

With what I have found, Potions trigger the glitch.