This started happening right after updating Space Exploration from 0.5.x to 0.6.x.

Relevant output:

Error MainLoop.cpp:1284: Exception at tick 112406179: The mod Crafting Combinator (0.16.3) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event crafting_combinator::on_tick (ID 0)
LuaRecipe API call when LuaRecipe was invalid.
stack traceback:
        [C]: in function '__index'
        __crafting_combinator__/script/cc.lua:326: in function 'set_recipe'
        __crafting_combinator__/script/cc.lua:191: in function 'update'
        __crafting_combinator__/control.lua:107: in function 'run_update'
        __crafting_combinator__/control.lua:117: in function <__crafting_combinator__/control.lua:109>

Second this, exactly same stack description:

The mod Crafting Combinator (0.16.3) caused a non-recoverable error.
Please report this error to the mod author.