Probably, the missing data is tagged with additional "reason" (look at the docs for the Missing syntax).
Maybe this example will help:
ds = Dataset[{<|"a" -> 1, "b" -> 11|>, <|"a" -> 2, "b" -> Missing["somereason"]|>, <|"a" -> 3, "b" -> Missing[]|>}]
ds[Count[_Missing], "b"]
2
ds[Select[#b == Missing[] &]]
ds[Select[#b == Missing["somereason"] &]]
ds[Select[MatchQ[#b, _Missing] &]]
