As far as I can see there is a quite complex grammatical structure:
כל חית is feminine כל עוף is masculine נפש חיה is feminine
Gesenius says that the personal-suffixes 3rd masculine singular in the phrases "יקרא-לו" and "הוא שמו" are to be understood as collective singulars (quote: "in Gn 2:19 לוֹ refers to the collectives ַחיָּה and עוֹף", see Hebrew Grammar §145.5)
If so why wouldn´t you expect the feminine singular personal-suffix form in order to agree with the feminine noun form נפש חיה? Of course the masculine form fits to include male as well as female animals.
Could it be mere poetic style? Is the reading and interpretation as straight forward as this verse is used to being read?