If you are flying on a connecting flight and you pay for the revenue for the ER seats does it apply to both flights?

My friends are flying SFO -BOS and BOS to EWR.. They were put into the ER on the first flight but the CO rep said they couldn't get it on the second flight.

I went into her account and I was able to put her into Row 21 without a hitch. What's the right answer?