I believe this is caused when you set a machine to upgrade to one with more module slots without having a machine to place, and setting the modules for those unavailable slots. encountered when upgrading from T2 assemblers to T3.

The mod Repair Turret 2 (1.2.2) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event Repair_Turret_2::on_tick (ID 0)
Index out of inventory bounds.
stack traceback:
[C]: in function 'index'
__Repair_Turret_2/script/repair_turret.lua:940: in function 'try_fulfill_proxy'
Repair_Turret_2/script/repair_turret.lua:750: in function 'check_target'
Repair_Turret_2/script/repair_turret.lua:1060: in function 'update'
Repair_Turret_2/script/repair_turret.lua:2910: in function 'check_turret_update'
Repair_Turret_2/script/repair_turret.lua:3188: in function 'handler'
core/lualib/event_handler.lua:72: in function <core/lualib/event_handler.lua:70>

This was caused by (on upgrade) referencing the new inventory while item was not replaced yet, I guess testing with infinite chests has its limits :D It now still accounts for the old item, and since you cannot ctrl-c different tier machines over old ones anyway it should not be a problem