I would definetely be on alert, xrays are not fool proof, a puppy could have been hiding. You could pull a progesterone test to see if she is going into labor or maybe try a sonogram instead of xray to see if you can detect a heartbeat.
We have never had a singleton not show up- in our experience, when there has been a singleton, it is a larger than normal pup and no way it could be missed.
Never missed a singleton, or small litter, with an x ray yet. BTW - if you haven't already, you may want to check her thyroid and do cultures to find out why she missed.