In late June we had reservations for the Vatican Museum. We arrived a bit over an hour early since we had read that the lines for picking up tickets can also be long. They weren't at all and we got our tickets quickly. Since our entrance time was an hour away, we decided to go walk around to St. Peter's which required exiting the museum entrance area. The lines at St. Peter's were way too long to wait so we returned to the Vatican Museum. There are two lines, one to buy tickets and one to pick up. Since we already had our tickets, we didn't want to get in the block long line to buy tickets so went in the line for pickup. The guards there didn't want to let us in! They looked at our tickets and told us we could only come in once. We explained that we had picked them up earlier but since our admission time was an hour away had left. They kept insisting we could only enter once. We kept arguing and the guy finally relented and waived us in. The bottom line of this is if you arrive too early to pick up your tickets, just hang around inside waiting your time!
Did you try to enter the museums right away or just assume you'd be refused? My memory's a little fuzzy about the details of whether my ticket time was checked at all (I did arrive early, but not by nearly that much), but I remember going up an escalator where there was a large shop, the audio guide rentals, a view of the Bramante staircase from the top, and access to a patio and a cafeteria.