While it is difficult to say what someone else means by a statement like this that can be taken in a number of different ways, it's very similar to another expression: "If something seems to good to be true, it probably is." In that case, the meaning is that if something is such a good deal that it seems unbelievable, it probably is not true. Here, the meaning is similar: There must be some hidden problem with a boyfriend that seems so perfect. There is a problem that we can't see.