Its not really "Logic" its just them not thinking it through or not caring. Why do people have to ask questions? They just want people to enjoy the game. Not worrying about how a Skitty or Wailord will do it... lol
Or how a Pokemon can learn Punch moves with no arms. You see they don't go into detail. I mean where does your mum or anyone for that matter apart from yourself sleep as there tends to be about 7 or so beds in each region or related to you question How do Pokemon do it...
Why would they go into all that detail when it will not affect the game play and that. Only 1 in maybe 1000 people will notice stuff like that :P
I'm sorry if this wasn't the answer you were looking for but honestly you will not get a better answer than this or the others as it is just a case of they are in the same egg group. There is no special reason for why they can mate. It just happens :P They probably just didn't realize this mistake.