Nevermind. I worked around it by moving the characters to a different group.
First of all, make sure your screen is big enough to see the whole editor. I've found if I don't maximize it, the right side of the screen is cut off.
Then go into your custom group and click on the character you want to delete, in the list on the right. A button labelled "Delete" should appear to the right of his name. That's why I said to maximize the screen, if you don't, it might be hidden. 
If it says "Base Group" or some such, that means you defined the critter as being in that group. Go edit the critter and put him in some other group. After you get through with all of that, you'll have to edit the mission to update the group list.
[edit] Ah, see you figured it out. Well, this post can be helpful for the information.
While tweeking my first published arc I added a new minion type to the two custom groups used in it and as a result it shot me right past the (wee frakkin' tiny) file size limits. How do you remove a single critter from a custom group?