flychic, you're right, unless somehow the layover is not considered by UA a break of the travel. The agent may have thought you were asking about needing only one per one-way trip.
If you have a traditional round-trip or open jaw, expect them to deduct one HK-49 on each "way". But check your balance on-line, as many posts will tell, UA may often deduct the wrong type of cert or the wrong amount. If that happens, Mileage Plus should be able to fix it.