If you put
“whonix file size for three files are not what the server reported”
into search engines you should fine existing discussions on that.
Size of file dists_jessie_main_binary-amd64_Packages.gz is not what the server reported
Same for searching for:
qubes Clocksource: timekeeping watchdog: Making clocksource ‘tsc’ as unstable because the skew is too large