How big of a gap are you seeing? In my experience, there is usually a 5-8% gap between Adobe data and other data sources. If the gap is more than that, then there is likely a problem. Unfortunately there are a lot of reasons why the data could not be present. Anything from implementation bugs to metrics/dimensions not being set up correctly could be the cause.
The first thing I would check is for patterns. Are there data gaps in other metrics too? Are the missing purchases happening in a particular time frame? Break down the number of orders by day or by hour, depending on what you're seeing, and compare that to your external data warehouse. This can tell you if maybe you're missing data from a specific time period.
If that isn't the case, I would then suggest looking at different customer types or order type (singed in vs guest, etc based on the options on your site). Being able to pinpoint specific variables that are present in all of the instances of missing data can help you determine what is wrong.
The way I usually tackle this is to eliminate one variable at a time. How did you check the test orders? Did you look at the data in a debugger or did you look at the data in workspace? Is it the total revenue amount that is off or the number of orders? If it is the total revenue, I would check for things like additional fees (eco fees or shipping/handling fees) that might be present in your external data but not in Adobe.
