Does it happen often? No. I don't encourage it, the players tend to avoid doing it themselves.
When it DOES happen, I'm sort of forced to up my energy and bounce between both groups to keep them engaged... and you can be sure that if one group gets into a combat, the other is going to as well.. or get into some hairy situation that needs them to be engaged. Maybe the two situations are linked in some way, though separate. I run them both on the same initiative track.
One big thing here is managing pacing and slicing time as you need it, so that if the groups are separated, and you think that there's something that they can both get engaged with, you cut time with each so that they happen to get into initiative at the same time.
For example: in spelljammer, the party boarded a ship. They found that the crew was all fast asleep, couldnt be woken up. They found one of the sleepers dead- they thought to conduct a dissection to see if they could determine cause of death. The two folk with medicine took the corpse to a table, other two kept exploring the sound they were hearing. Jump between each group, describing what they're seeing, answer some questions, not letting either side spend too much time unengaged.
Now I know that there's a hag and a feyr on this ship, they're the cause. The feyr's busy eating the sleepers, the hag could jump the medicine PCs anytime.. but I wait until the exploring PCs find the feyr chowing down- as those PCs are about to find the monster chowing on sleepers, THAT is when the hag shows up as a creepy girl and tries to fk with the medicine PCs... she messes with them a bit as a creepy girl, switch back to the PCs discovering the feyr. It's unhappy to be interrupted, roll initiative. Switch to the PCs with the creepy girl, who reveals herself as a hag and they can join the initiative.
Start combat.