Why are they called "Bnei Ir"?
'Rashi': Ezra, the author, did not know whether or not they are Bnei Binyamin. Therefore, he wrote them by themselves. Also, he was unsure because it says "u'Machir 1 Lakach Ishah l'Chupim ul'Shupim" (15).
Radak: Ir is Iri ben Bela (7). Malbim - Chupim and Shupim were Roshei Avos.
Machir was from Menasheh (14-15).
Why is Chupim called "Bnei Acher"?
'Rashi': Ezra was unsure if they are Bnei Binyamin, so he wrote them by themselves.
Radak: Perhaps Acher is a second name of someone mentioned above. Ezra was concise - he wrote what he found, or what he knew from tradition.
Malbim: It says Bnei (plural), for Chushim had brothers included in his Beis Av.
