I've run into this before, but don't remember how it happens.
There is something significant about a folder with a blue arrow vs. a red pushpin. I can't remember that, either. It could be that the blue arrow is a "past" trip and the red pushpin is a "future" trip. Or not.
To fix it, try to drag and drop the "hubs" (NE3, NE4, etc.) from one trip folder to another. Once one of the "NE" trip folders is empty, you can delete it.
I haven't had to run BaseCamp for a few months, so am a bit rusty.
2008 Holiday Rambler Admiral 30PDD (Ford F-53 chassis)
2009 Honda Fit Sport