This does appear to be a bug. I will add it to our tracking database.
It's unlikely to cause any problems (which is probably why it's gone unnoticed for so long) because the types involved are also loaded by type palette files so they will still be in the global type list as long as those type palette files are loaded (which is usually for the life of the process). Also, when you save the file, the types that are actually used by the file will get added to the file's type usage list automatically if they weren't there already. You can see this if you save the file after doing what you've said, then go back to the type palette view for the file (NOTE: You will need to select a different file and then re-select the file to force the view to refresh if the file in question was already selected in the type palette's view).
Because a user can programmatically edit a sequence file and might forget to or not know to call TypeUsageList.AddUsedTypes() when adding instances of previously unused types, this is somewhat of an expected case that TestStand tries to handle.
Hope this helps. Let me know if you have any additional questions regarding this.
-Doug