There are mainly two reasons for PPC deviations:
1. Seller Central vs API: Databases with Differently Timed Updates - Cleansing of Bot Traffic
Amazon will update and correct the data for Sponsored Products over the course of roughly 7 days after an event, so that the impressions and clicks will, for example, be cleansed by the traffic which resulted from Search Engines or Bots.
This data may be updated in slightly different times for Amazon's two channels (Seller Central & API), which can lead to slightly different data outputs within the first week or so.
2. Lagged Allocation of Orders & Clicks
Sales will often only be attributed to the respective clicks with significant delays, as many customers will only buy the product several days after clicking on the ad. This Allocation can also be updated for the two channels at a different pace.
After around 7 days most sales should be attributed to the respective clicks.
Recommended Timeframe for Optimizations: Two Weeks before Current Week
It is recommended to not consider the current week for any PPC analytics. This will also minimize the risk of falsly moving keywords to the Negatve Keywords list, as many of its sales may not yet have been connected to the clicks of that keyword.
This is why the PPC Manager offers a button which wll directly set the timeframe to the two weeks before the current one: