The usual reason for something like this is that there is something in there making them separate. The most common is a bursa. A less common reason is something like rheumatoid arthritis. Suggest you get it checked out in case it is one of those uncommon (and more serious) reasons. If it is just a bursa, then the treatment is simple and straightforward with something like a metatarsal pad under the metatarsal heads.

Mortons neuroma is what caused my #2 and #3 toes to separate according to My PCP and podiatrist. Weird feelings in my right foot. High impact exercise causes pain and my foot feels like it has rocks in it, not a pebble! Always feels like my sock is bunched up in shoe. Also my foot gets numb and other weird shooting pains. My toes are really spread apart! Also have a hammer toe. Wider shoes , footbeds, and metatarsal pads, have helped. Still the symptoms persist and seem to get worse over time.