I've been a happy jodohost customer for several years now but never remember being charged for the stopgap domain. I forgot about the files (no excuse I guess) included there, and this year my bill is 20-odd dollars higher than normal.
I believe they are treated like any other domain, so if you are on a shared domain that has a domain limit, the stopgap will count on that limit and could trigger the $2/m charge. This hasn't changed recently, it was quite a long time ago, over a year since we changed the plans.
Could it be you added a domain, and the next time a billing cycle came around it triggered this and it selected the 'stop gap' as the one to bill extra on the line item?
We have started enforcing some billing policy about 7 days late and get suspend, as we had been allowing some people to go for a very long time with a negative balance, but that would not affect you here.