That's the point. Three million is how many EU citizens supposedly lived in this country. There even formed a pressure group to represent them called #the3million
https://www.the3million.org.uk/
So far over 5.6 million applications have been received and over 5 million processed (any that apply today are ok even if not processed yet).
So millions of extra people living here that we didn't know about officially have been discovered via this process. No wonder house prices have been astronomical.
The Census this year will be interesting when it comes out to see how it matches.