our company is small. when I applied to my husband's place of work, we couldn't be together in the same department. I needed to apply to a different dept. so i guess it is not uncommon.
It's mainly if you are in a relationship with someone who is your boss. It would seem like they are favoring you over others, and people could use that against them. They wouldn't care if the were both ordinary employees, but they are boss and subordinate.