It seems to be related to the teleporter. I reloaded an autosave and mined the mobile teleporter, then the error did not occur anymore.

MainLoop.cpp:1183: Exception at tick 3219375: The mod Warptorio caused a non-recoverable error.
Please report this error to the mod author.

Error while running event warptorio::on_tick (ID 0)
LuaEntity API call when LuaEntity was invalid.
stack traceback:
warptorio/control.lua:616: in function 'transfert_energy_use'
warptorio/control.lua:521: in function 'transfert_resources'
warptorio/control.lua:556: in function 'entrance_transfert_resources'
warptorio/control.lua:569: in function 'logistic_update'
warptorio/control.lua:307: in function <warptorio/control.lua:304>
stack traceback:
[C]: in function 'index'
__warptorio/control.lua:616: in function 'transfert_energy_use'
warptorio/control.lua:521: in function 'transfert_resources'
warptorio/control.lua:556: in function 'entrance_transfert_resources'
warptorio/control.lua:569: in function 'logistic_update'
warptorio/control.lua:307: in function <warptorio/control.lua:304

It is related to the teleporter yes. There must be some cases the mod is not handling well, it's either from warping or upgrading the logistic, I will try to find out.