他们有不一样的地方吗that means what difference between them, which is a question to ask the difference rather than a certain place of them, so the place is translated difference, in Chinese we say "不同之处". 有不should not translate into have not, both 有 and have are verbs, they have the same meaning, while 不 is not like NOT. Not is JUST a adverb,不 can be used as adverb,or keep single meaning, even put in an end of a question. In your example, 不 is used to negate 一样，not same that is different. Your translation may be "Do they have no same place? "