I think Ellie was probably a little overwhelmed by her freedom, or thought that something was wrong since her normal nighttime routine had been changed. If she's happy in her x-pen at night and there's no reason to let her roam at night, I'd keep her in there. If it ain't broke, don't fix it!
I keep my Bella in a crate on my nightstand at night, and will probably keep her there for the foreseeable future. There are too many things she could get into if she were left unsupervised at night...