PokéBase - Pokémon Q&A
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OK, my Porygon and Ditto are in the day care... 1 Hour later they tell me "They're doing fine. The two don't seem to like each other much".
In the next thirty minutes I get the same reply. I got bored so I went to the Pokemon league and beat the champion, went back to the day-care and got the same reply. WHAT AM I DOING WRONG???

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You're not doing anything wrong.

The message you get just means that you are less likely to get an egg from the two. It's just back luck, so keep at it and it'll work eventually.

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According to this, you have a 19.8% chance to get an egg from them.


Source
Hope I helped.

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This has become quite a bit of an issue these days, feel like this answer is important for them :P
going to the pokemon league also doesn't get them very many steps.  when i'm breeding i tend to read something and bike back and forth in front of the guy.  just wish he said something when he had an egg like he did in gen5.