It is likely a statement about not receiving miles (or hotel points) for the stay itself. Actually that is one of the reasons never to use expedia anyway, often the rates are almost the same compared to directly booking on the hotel's own website, the cancellation conditions and charges are usually worse, and you don't know for sure if you get miles/points for your stay.

I looked at the T&Cs for the 'flight & hotel' bookings on the BMI website and didn't like those either. Technically you aren't buying your flight directly from BMI, as the entire package is sold by a travel agent.

BTW: Welcome to FT