I had the same thing happen using US Air Miles.

In January I booked 2 ticketsSFO to Sydney (Via Japan), using miles from two accounts...In March I noticed only one account had miles deducted, but I had paid Taxes on Two tickets with only one $50.00 partner fee charged.

After waiting a while, I decided it wasn't worth worrying for the next 8 months weather or not they would just cancel the one booking, and mess everything up. (we have all read the horror stories with US Air and their Fraud Dept. ) So I called and yes they confirmed they did miss it, and promptly removed the miles.

Sometimes honesty is the best policy!