Edited to use public dataset
I have a table with the following schema, which you can access here: https://bigquery.cloud.google.com/table/reals
If a query can be interpreted in many ways, BigQuery will do its best effort to guess what were your intentions - producing sometimes non-congruent results. This is true to every database, since SQL has space for these ambiguities.
Solution: Eliminate ambiguity from your queries - probably both results are correct, depending on what you are trying to count.
(eliminate ambiguity by not using *, and making the prefix explicit, while you could also make a explicit request on which ways you want the table flattened)
I would really like to comment on your specific data and results, but given that you haven't provided a public sample, I can't.