This certainly happens, and cutting between one or more scenes is a crucial MC skill.
On the other hand, the more PC-NPC-PC triangles you create, the more likely you are to have good ideas for scenes that involve multiple PCs.
Even then, you are often going to have PCs isolated for various reasons -- but if there are triangles and strong relationships in place, then when one of those NPCs shows up in another scene, it's almost like the PC is present, both in terms of fictional consequence and in terms of player interest.
Like, if we've established that Balls is second in command of the Chopper's gang, then whenever she shows up in a scene with the creepy Brainer, it doesn't matter whether the Chopper is actually off on some 'mission' somewhere -- everyone knows that how the Brainer interacts with Balls is going to directly affect the Chopper (and result in consequences for the Brainer, probably.) The Balls-related triangle creates interaction at a distance, and the scene is no longer isolated from the other players.