You should be able to delete, no problem.
Just took a look at this.
The seasons festivities mean I'm not totally sober right now.
But I can't reproduce this issue with the current version of code I have.
I found a different problem with the save file name, which I've fixed and pushed the changes.
That will be delivered the next time Ezra puts a copy of the installer on the server.
I'll take another look tomorrow.
Maybe an old version of one of the libraries was distributed somehow.
The background to that "old" bug:
The unit structure you see units represented in for the treeview relies on the xml file structure.
A unit has a collection of subordinates which in turn has a collection of subordinates and so on.
When you delete it needs to go find the parent unit in order to take your unit out it's list of subordinates.
This is done by taking the CO Id property and taking a look for a unit with a matching ID.
When that wasn't set or two match then bad things happen.
You could open an xml file using internet explorer ( or an xml editor ) and check the IDs of one of your files are OK.
Or
Just click the renumber button and it'll redo the ids.
Since you don't have the scenario editor yet, the specific ID of a unit doesn't matter so much so long as they are consistent within the hierarchy.
When we eventually distribute the scenario editor then it'll matter... But we'll hopefully have worked out what's happening and fixed anything needs fixing by then.