The correct answers are: We hired five new software engineers, three of whom insist on sleeping under their desks. We hired five new software engineers; three of them insist on sleeping under their desks. We hired five new software engineers, and three of them insist on sleeping under their desks.

When connecting two independent clauses, you cannot simply use a comma and a pronoun like "them" (this creates a comma splice). You must use a relative pronoun after a preposition (three of whom), use a semicolon (; three of them), or add a conjunction (, and three of them). Also, remember to use the object pronoun whom rather than who after the preposition "of".