Reproducible. Sending map save. -- may be related to my earlier report (configured remote in filtered hotbar slot) If so, I know that you are looking at it.
Get SP2 from inventory and drop into (or open the ASSY and replace SP1 with SP2) the ASSY3 making Electric Engines.
[edit - the assy3 making Engine Units do not seem to have this issue, just any making the Electric Engines]
[edit - If I remove the SP1 then add SP2, all seems OK!]
Core v1.1.2
Mod v1.7.1
Same modlist as before
120425.595 Info AppManagerStates.cpp:1930: Saving finished
120614.120 Error MainLoop.cpp:1281: Exception at tick 23928956: The mod Spidertron Waypoints (1.7.1) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event SpidertronWaypoints::on_player_main_inventory_changed (ID 32)
Inventory slot is not empty.
stack traceback:
[C]: in function 'newindex'
__SpidertronWaypoints/mode_handling.lua:30: in function 'convert_remote'
SpidertronWaypoints/mode_handling.lua:132: in function 'convert_remotes_in_player'
SpidertronWaypoints/mode_handling.lua:135: in function <SpidertronWaypoints/mode_handling.lua:135>

Sure, I'll take a look, but if you still have a waypoint remote filter in your inventory then that is still the problem. I don't yet know why it only occasionally causes a crash instead of every time you change your inventory, but it is definitely causing the crashes.

I understand the risk.
I do maintain the remote filter slot. It is more convenient than configuring it every time I use it.
If issue begins to outweigh convenience, I will remove the filtered slot.

Thank you.

Yeah I see the issue. I guess I tried to be too clever with the remote icon switch-with-mode and now I'm paying the price because it doesn't work properly with filters! I'm working on a solution now :)

Fixed in 1.7.2. See https://mods.factorio.com/mod/SpidertronWaypoints/discussion/5fd4598f5860836bc4dc3a96 for more discussion.