With this setup, taking the cube out of the Synthesizer with an inserter crashes the game.
https://i.imgur.com/bWqrOm0.png

Hi, please make sure you are on the latest version. If the crash still happens, please give me a list of mods you are using or a save file - it is very likely that the problem is being caused by some other mod you have active.

I am using the latest version of the mod.
Modlist:
AAI Loaders
AAI Vehicles: Flame Tumbler
Afraid of the Dark (enforced ...)
Alien Biomes
Alien Biomes High-Res Terrain
Auto Deconstruct
Balanced Waterfill
Biter Trails
Bottleneck Lite
Bullet Trails
Clean Floor
Disco Science
Early Entity Ghosts
Easy Start Research (Custom mod, just adds 2 researches to get a bigger inventory and speed up bots)
Editor Extensions
Electric Trains
Factorio Library
Flow Control
FNEI
Krastorio 2 Assets
Module Inserter Extended
Ore Manager Fixed
P.U.M.P
Power Armor MK3
Project Cybersyn
Pushbutton
Rate Calculator
Recipe Book
Recursive Blueprints
Renamer
Research Progress Frame (1.1)
Santa's Nixie Tube Display
SE Beacons (Custom mod too, changes beacons to be like in SE)
Show Max Underground Distance
Simulation Helper
Squeak Through
Stats GUI
Text Plates
Train Trails
Ultracube
VehicleSnap
Wire Shortcuts
YARM - Resource Manager

ok, that's quite a list (and there's a bunch that seem like they won't do anything with ultracube anyway).

It could take some time to figure out which one is causing problems. I would recommend for now starting Ultracube with a smaller/more curated mod-list and add the ones you actually need as you go, rather than just throwing in everything you usually use. That way if you start seeing script errors it'll be more obvious which mod might be the problem (i.e. one that got turned on recently).

Running the command /cube_refresh in the console should fix things if some mod has messed up the game state, but if the problem mod is still active it could mess it up again any time.

I am currently running the mod and just removed all the mods that impact gameplay in a bigger way (Alien Biomes, Balanced Waterfill, Disco Science, Early Entity Ghosts, Flow Control, FNEI, Ore Manager Fixed, Power Armor MK3, SE Beacons, YARM - Resource Manager). No problems so far

Alien biomes should definitely be fine for what it's worth.

Most of the other mods you listed don't look too suspicious, either. Please do feel free to add some of them back in as you go, maybe just do it bit by bit so the culprit can be found more easily if you start getting errors again. Thanks.

My guesses are SE Beacons (custom modified version of Beacon Rebalance), Power Armor MK3 and maybe Disco Science

Ultracube has custom beacons that are similar to SE by default anyway, so you don't need that one. Ore Manager might be suspicious (I'm not sure)

The Ore manager is a mod i still had activated (i dont use it, used it once) and it allows you to pick up an ore patch with a special chest and place it down somewhere else