That's pretty much always the case when one person hires another person to do something. The hire-er wants to get as much work done for as little money as possible, and the hire-ee wants to get as much money as possible for each unit of work. They're polar opposites, yet this arrangement happens all of the time.

The problem with having different incentives is when one party doesn't recognize that there is a mis-alignment. If you're selling your home and you don't realize that your Realtor's time is not an endless, worthless resource at your disposal, then you may be inclined to insist on your Realtor spending endless hours of aggressive negotiation, potentially putting the offer at risk of closing at all, for an amount of additional money to you that's not really going to make much of a difference to you. (My wife's been involved in deals where one party or the other has risked a deal that's been in the works for 2-3 months over less than 0.1% of the house's value.)