So - a few things are confusing:

When you said "offered a few hundred dollars for upgrade", United does not have a cash-only upgrade waitlist program. It's either buy-up to the next cabin and confirmed, or use miles + copy for upgrade (most likely onto the waitlist).

Also, on buy-up on a connecting itinerary, in general it's done on a segment-by-segment basis, not the entire itinerary.

Review your upgrade purchase receipt and it will show you which exact segment you purchased your upgrade.