Because he was the one that carried the child and calling both parents dad can be confusing so I guess he just called him "mom" bc he basically is the mom
Anyone regardless of gender can get pregnant. I read an omegaverse story where a male alpha got pregnant. http://www.mangago.me/read-manga/sukijanaitte_hyakkai_tonaeta/
In omegaverse stories, they call the parents "mom" and "dad" in regards to who fathered and who mothered the child, even if the "mom" is a man. They do the same thing in Sex Pistols, though that story isn't technically omegaverse.
I was so confused by the Mizutani's "mom" and then they using the pronoun "he". Why didn't they just say "dad"? ┑( ̄Д  ̄)┍