I've enabled ipv6 on my ubuntu server recently and it was 100x slower. The only solution I found is to go back to ipv4: https://askubuntu.com/questions/759524/problem-with-ipv6-sud...
I just updated from 2001:878:346::116 / mirrors.dotsrc.org; no problems.
Which mirror were you using, and did you file a report?
If the former I'd image this is a kernel bug and has nothing to do with any Ubuntu servers.