It sounds like a play on words: "to miss" can mean "to yearn for", "to arrive too late(or leave too early)" or "to fail to hit". I guess he hadn't seen her for a long time and yearns for her company: he misses her; however, the chance was lost by his late arrival: he missed her.

Out of context I'm not sure but "He misses her" normally means that he feels a need to see her, talk to her, or something like that. He wishes to be with her in some form. "he missed her" probably means he had a chance to see her, but did not for some reason. So, he wants to see her, but for some reason he did not.

Out of context it means nothing. Do provide.