To reproduce: load a save with personal logistics available, enable "trash unrequested" (and make sure the cube isn't requested by the player), pick up the cube and hold it in your hand, and open the map view with 'm'. For me, this prints the messages "optimized cube control routines failed" and "cannot find the ultradense cube". The cube isn't actually gone, it's just placed in the player's trash slots.

I have a few other mods enabled; if I disable everything except Ultracube, I still get the second warning message above, but not the first. The other mods I have are: elevated rails, pushbutton, textplates, UPSFriendlyNixieTubeDisplay.

I found another way to trigger these 2 messages, which doesn't seem to require personal logistics: pick up the cube and hold it in your hand, and click a locomotive. It'll show the same messages as above, even with "trash unrequested" disabled.