You can and should contact them and ask them to grant you a deferrment for that time and remove the lates.  Be prepared to send them proof that you were enrolled full-time on the dates in question.

That said, it is your responsibility to make sure your lenders are aware of your "in-school" status and that your loans are properly deferred, especially when you change schools or take a break and return.  Normally, lenders are notified automatically, but there's always the chance for a mistake.  Hopefully, they'll be willing to work with you on this.