Of 28,811 target URLs, 1570 have an error for the primary scan, but complete the not found scan fine.
Of the 1570, 1277 (81%) are timeouts. This would seem to indicate that what is often at issue is some JavaScript or something that is on the homepage but not on the 404 et al page that is not loading in a timely fashion.
Also, think through and confirm behavior of results if a status code other than 404 or 200 results.