what is the reason for this multiple domain result?
Because proteins can have multiple domains, and proteins from different families can share domains. The Wikipedia page on protein domains is a good introduction, and you will find there an extensive literature review.
how to identify which one is best one?
As proteins can have multiple domains, there may be no "best" domain. Of course, one has to filter false-positives, but this doesn't mean one will end up with just one domain per protein.