What causes discrepancies?
Discrepancies are a by-product of counting methodology. In other words it's the difference between when a Publisher considers an Impression "counted" and when the Third Party considers the same impression "counted". Additionally, different vendors may count their impressions at different times in the ad delivery process so discrepancies can vary by vendor. Here's another way of looking at this:
What is considered a normal discrepancy?
Agencies and Publishers typically consider a discrepancy of up to 10% normal, and most vendors will not troubleshoot anything less than this amount. My experience has been that most discrepancies range 2% - 5% depending on the vendor.
How do Publishers compensate for discrepancies?
When trafficking a campaign that is billed using 3rd Party numbers, a Publisher will "overbook" the goals on the campaign by a default or anticipated discrepancy percentage to ensure that the Advertiser's contracted goal is met.
For more on discrepancies you can read about the Impression Exchange Solution: An industry-wide standard mechanism designed to create immediate awareness and transparency around discrepancies.