Look, we are actively working on support for a subset of the happy eyes
RFC that works around issues like that. Your system is still likely
configured wrongly somewhere, though. I and many others run apt on
IPv4+IPv6 systems with non-routable IPv6 and we do not have a problem.

Note that this is not a problem of apt. Your system is configured to try
IPv6 first, so any application not implementing happy eyeballs has the
same issue. Some applications only try the first address returned by
getaddrinfo() - they will fail hard on your system. The key takeaway is
to configure your network and/or NSS settings correctly so all
applications work.

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https://bugs.launchpad.net/bugs/1740114

Title:
  apt's IPv4 fallback in case of a malfunctioning IPv6 connection works
  horribly

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