Ideally if you didn't have any amendments for the events, then 'Download Filename Instances' should be equal to the 'Custom Event'. If you use some amendments like getValOnce, Event Serialization etc., you will see that the numbers are less than Instances(Which will fire every time).
Check whether Custom Event is firing every time you are downloading the a file.
There are multiple reasons why we do not see the similar or close number in File download report and Activity map.
As File Download work explicitly where s.tl() call is implemented. Whereas activity map may or may not fire on the link where file download is firing. Below is the document that will help in understanding activity map link tracking
Link Tracking Methodology You can check in debugger if activity map is firing when file download is firing. If they are firing, I will suggest you to please contact customer care so that they can investigate in detail.