a, the bees are not female.
b, the butun aren't female either.

The correct translation according to context is 'their bellies'. Your translation is absolutely correct.

What you are confusing is the ha. Butooniha is written like this :
ﺑﻂﻮﻨﻫﺎ
This 'ha' at the end, is a pronoun, singular feminine in form but translating to plural (them). This pronoun coupled with the previous noun (bellies) indicates possession. So, butoon = bellies, ha = their, butooniha = their bellies.

You are confusing this type of ha with the other type which feminizes a noun. That one occurs in writing in these four forms
ة ه ﻪ ﺔ
It is usually referred to as the Taa Marboota

A noun like Nahl is masculine. Adding a Taa marboota at the end (Nahlah) makes it feminine.
ﻨﺤﻞ
Nahl means male bee
ﻨﺤﻟﺔ
Nahlah means female bee

Like I said, grammar is confusing and large doses can be hazardous to mental health. If you don't get it, don't worry. This isn't really beginner level grammar.