I am facing the same problem in Ubuntu 20.04 LTS ( 5.4.0-33-generic
#37-Ubuntu SMP Thu May 21 12:53:59 UTC 2020 x86_64 x86_64 x86_64
GNU/Linux) , Gnome-control-center 3.36.2 .

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https://bugs.launchpad.net/bugs/1717466

Title:
  Proxy settings are missing in apt.conf

Status in gnome-control-center package in Ubuntu:
  Confirmed

Bug description:
  Description:  Ubuntu Artful Aardvark (development branch)
  Release:      17.10

  When proxies are set via network settings dialog this does not affect 
apt.conf.
  This results in software installation and upgrade problems.

  I had to specify proxies by adding "Acquire" in apt.conf.

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