I haven't had that problem in either of my playthroughs. Your problem could stem from Rikku and Yuna being dead at the end of battle which they would not gain any experience. Another factor could be, if I recall correcltly, that there are some accessories that halt EXP gain and perhaps you had them equipped for some time creating the gap. Paine could have an accessory that increase EXP gain but I don't think there is such an item in the game to begin with. It could be a glitch of some sort though I'm not inclined to believe that. Perhaps the reasoning is simple but you have forgotten how it happened. As long as you keep on winning battles there should be nothing to minutely fret over.