He has his ways

In the first episode of the third season of the tv series ,"The Mentalist" .The wife of the victim (Driver to the abducted Harvey Dublin) says ,"He had his ways".

Now ,I’m not quite sure as to what to make of this phrase here . I mean, normally ,one would think that the person being talked about has certain methods to achieve a particular goal ,but the problem with that interpretation is that this phrase is followed by a further prod from Lisbon ( The adorable,constant companion of the protagonist ), which is subsequently followed up by the victim’s wife with ," he had a temper " .

Well, I’d like to think it means that he had certain ugly aspects him or that he had certain quirks ,but I simply had to double-check . I would appreciate any help on the matter ,thank you.