Sometimes both of mine have a big belly at bedtime if they've eaten well that day but not done much in the way of pooing. For them it generally means they'll have a big poo 1st thing in the morning and perhaps a few times the following day. They don't have any known allergies or intolerances. I don't know if this is what you mean, sorry if not.
I thought that it was down to all the internal organs packed up tightly in to their teeny tiny little tummys <gets a bit gooey at the memory of squishy tummys> Although I could be wrong. My Dts have got flat stomachs now, they always had a little pot belly, it only disappeared in the last 6 months or so, they're 4.
Both my DDs had round pot bellys as toddlers, it disappears as they grow.
Also, I noticed their bellies would get really big and round (like they had a football in their belly!) for a week or two just before they had a proper growth spurt and grew a few inches/went up a clothes size!