Is this mostly true?
It varies widely, but it certainly can happen.
The normal practice is to excavate until the yield drops to nothing, then do another level or two just to be sure. Often, an auger is used to get another meter down just in case.
Many sites have clear bottoms, with rock or other layers, but when you are in soil deposits you don't have that.
It is common to use a backhoe or other mechanical device to sample the stratigraphy of a site on a major project, but when you're in a cave or down 5 meters, that is not always possible.
So, yes, the lowest layers can be missed if there is a sterile layer between cultural layers. In areas of heavy soil deposition a sterile layer can be several meters in thickness. And, when you are dealing with sites of some reasonable antiquity, there will often be fewer cultural materials, they will cover a smaller area than the overlying sites, and they may be much deeper.
Its enough to give us nightmares! (I like it when I hit a solid rock layer, as then I know there's nothing else down there.)
Mostly true?
I'd say it defined the current state of scientific academia quite well...
My/our theory maintains that...(the earth is flat/square/roundish/tarnished, warming/cooling/flipping over/over populated/under populated/ whatever is popular)....and dissent will NOT be tolerated!