Pet odor! The more you know, the more you can potentially save! A close family friend is looking at making their first purchase and asked if I would tour homes with them. We walked into a property and right away I could smell cat spray/urine!! I noticed everything had been newly painted and the carpet was new as well.
From my experience from managing property apartments with this issue, replacing the carpet and pad isn't enough. Most likely it has been absorbed into the sub-floor. I highly recommend that you seal the floor, let it air out and reassess prior to installing the new floor. Recommend at least two coats. While the existing seller tried to do what was best it didn't solve the odor problem and whoever purchases the property is now going to have to rip up the new floor or learn to live with the smell. If the seller offers to have the carpet cleaned. You can request the carpet to be cleaned and then go reinspect it a few days later. Some odors could be surface but you want to make sure! This is good to know so you can ask these questions when you're looking at new potential property!
On the low end you're looking at $3 a square foot but on average most are spending around $5. If it's 1,200 square feet you're looking at $3,600-$6,000 to have it replaced. Add that to your negotiation tool box ;)