The mod Machine Upgrades (0.69.4) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event machine-upgrades::on_configuration_changed
Error when running interface function machine-upgrades-techlink.add_upgrade_data: Error when running interface function machine-upgrades-techlink.add_technology_effect: machine-upgrades/script/beacon-manager.lua:37: Something stopped us from making a special beacon. Alert the mod creator of how this happened.
stack traceback:
[C]: in function 'assert'
machine-upgrades/script/beacon-manager.lua:37: in function 'try_get_beacon'
machine-upgrades/script/beacon-manager.lua:49: in function 'update_entity_moduling'
machine-upgrades/script/beacon-manager.lua:104: in function 'to_call'
machine-upgrades/script/entity-modifier.lua:64: in function 'try_apply_modifier'
machine-upgrades/script/entity-modifier.lua:77: in function 'apply_auto_modifier'
machine-upgrades/script/technology-linker.lua:221: in function <machine-upgrades/script/technology-linker.lua:181>
stack traceback:
[C]: in function 'call'
machine-upgrades/script/technology-linker.lua:254: in function <machine-upgrades/script/technology-linker.lua:248>
stack traceback:
[C]: in function 'call'
machine-upgrades/script/automatic-tech-linker.lua:59: in function 'config'
machine-upgrades/script/event-lib.lua:124: in function <machine-upgrades/script/event-lib.lua:123>

Tried using different versions of Rubia and Machine Upgrades but still not working, tried the latest version of Machine Upgrades as well

Thanks for the report. I’ll take a look at it later today.

In the meantime, I need some additional information to fix this bug:
1) Could you confirm that the error report you get on the most recent version of Machine Upgrades is the same?
2) Does this happen at startup (first frame of the game) or in the middle of the game? If this happens when you build something, please let me know what exactly was built, and if there were any restrictions there I should know about.
3) If you turn off all other mods and boot your save, does this error still happen?
4) A savefile and/or list of mods you had on would be helpful for me to reproduce the bug. Otherwise I won’t be able to quickly fix it.

I conversed with several modders, and it seems like:
1) Another mod is destroying this mod's hidden beacons while it is still being created.
2) Doing so is such a major compatibility nightmare that it is that mod's responsibility to fix it.
3) We'd need to identify the mod first to tell that modder to fix their mod.

We worked this out on discord. You no longer have the problem, and can’t reproduce it. I’m closing the case until the day that someone else has the same issue, to provide a way to reproduce/test/fix it.