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