I have not checked the zip-file, but from the picture it looks like the export settings for the drilled holes is different compared to the copper, solder mask, outline etc.
Are you exporting the drilled holes using Excellon format? If so, then start looking into the settings for origin.
- Absolute or relative? Probably want it to be relative to the board outline, not absolute to the ECAD's origin.
There are also other settings, like inch/mm, leading/trailing zero suppression, number of digits, but in this case the board size matches with the drilled holes, but with an offset.
Another option for export is to use GerberX2 to get all your files in the same export.