Blanks in any Geocorr output indicate the absence of the source or target geography. In your example, 3, 9, and 2 are the number of persons in districts 101, 103, and 105 respectively that are not in any ZCTA.
For geo types without 100% coverage, Geocorr should show something like "[not in a place]" for the area name and "99999" for the code if the area is missing. I can add that to ZCTAs as well.
You can email me direct with questions about Geocorr. riceg@missouri.edu