The QC could be an old one resealed perhaps with an entombed worker bee? If the eggs are close to the bottom of the cells it could be a queen just getting her act together. Near the top of the cells is a sign of laying workers but takes maybe 5-6 weeks of queenlessness first.
This would worry me too, but I've been told that new queens often lay a bit erratically (one of mine was laying on top of pollen as well as in queen cups)... but sort themselves out. An egg in a queen cup, especially with a newly mated queen, is not time to worry.... but a larva.....well we have a problem.
I'd check in a few days. I would put my money on there being no problem then. If you don't see larvae in queen cups snuggled up in white goo, your queen is fine.