The K key or using the tool bar icon didn't remove units. Think it had something to do with the tunnel rats underground movement. It came back a turn later, not sure what series of actions made it happen and then start working again.
You can see the remove units is highlighted in the tool bar but units still present.
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Enjoy when you can, and endure when you must. ~Johann Wolfgang von Goethe
"Be Yourself; Everyone else is already taken" ~Oscar Wilde
*I'm in the Wargamer middle ground*
I don't buy all the wargames I want, I just buy more than I need.
In 3D, [K]ill Units leaves both unit outline and unit base showing. (If you want to hide the unit base, you need also to press the Toggle display of bases button, or hit the B hotkey.) In 2D, it shows an empty box outline. That is all WAD.
I never use the 3D if that makes a difference. I can't point to anything in particular triggering it. I simply will play a few turns into the scenario's listed and eventually either pressing the button or using the hotkey will no longer remove the units from the map. The button does light up so I know the command is making it through but the units don't remove from the map. It's a pretty frustrating issue because it makes it really tough to see IP's and trenches etc.