If a delete row (i.e. DeleteFamily) occurs at the same timestamp as an upsert (i.e. Put), then the delete must mask the puts, regardless of when the mutations actually hit the server. Currently, this is a problem if the delete is processed first and the upsert ends up writing a row to the index table when it shouldn't.
PHOENIX-4058, we cannot work around the issue by setting STORE_NULLS to true.