well, assuming you arent getting the message of brimming with energy or prefering to play with other pokeon, then if they dont get along message is fine. They still mate, sometimes it just takes a tad longer....
If they are getting the message of they dont get along, and you want it to change, tehn take them both out, and leave them in your party together, and do things to tame them, supposedly that works and upgrades their like for each other. Never really tested it to see if it works though