I have seen this before and guessed that there is an upwelling groundwater feature (known to neanderthals as a "spring") that is jetting up out of narrow fissures in the strata and this displaces the soft flocculent sediments and this creates these craters.
But there should be a "rim" around each one if that's the case?... so not sure my theory holds water.
Holds water... hee hee.