It happened to me last week, on February 28.
I had taken advantage of using some of two different promos, and when they ended, I still had 11 free listings from my usual 50 free per month.
I was working on a listing and noticed the .30 fee, so I saved it as a draft and called eBay.
The reps kept escalating it, and finally, the third rep i talked to said yes, there was a glitch on the eBay system and that LOTS of people were calling. She said it might take 24 hours to fix, so that I should wait to list. I pointed out that doing so would mean I would lose my 11 remaining free listings, as 24 hours would be March 1. She said she saw what I meant. So, she told me to list and she would call the next day and credit all the fees. However, when I checked about an hour later, the issue had been fixed, so I did my 11 listings. The rep kept her word and both called and emailed me, and said that since the issue had be fixed, she didn't need to refund me.
Long story long, I would call eBay to have them check into it.
