The mod Aquafarm Extended (1.1.1) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event AquafarmExtended::on_configuration_changed
AquafarmExtended/control.lua:27: table index is nil
stack traceback:
AquafarmExtended/control.lua:27: in function 'buildFishProductEntry'
AquafarmExtended/control.lua:37: in function 'buildFishProducts'
AquafarmExtended/control.lua:55: in function 'actuallyInit'
AquafarmExtended/control.lua:118: in function <AquafarmExtended/control.lua:117>

Disabling that or Factorio and Conquer: Tiberian Dawn clears the issue, both worked together before the update.

Reverted to F&C:TD Version 1.1.18 and its working with both mods enabled, no error.

Checked it out, this is because our hidden target dummy for the new Sonic Emitters is an invisible fish entity.
But it seems like Aquafarm Extended crashes whenever there is a fish that isn't mineable. They have a block of code that is supposed to handle it, but it has a bad index so it will never work. Should be a 1 line fix for Honktown.

I did a fix.