If you had sent them as separate items they would have complained that they should have been combined and they want a refund on the extra postage.

Send them an email thanking them for helping you to better understand the seller rules, and that you will sending them a cheque for $0.00 to cover the free postage cost of the second item. 

Get ebay to remove the neg when it happens, and don't forget to add them to your blocked list then move on.