I also encountered this bug on Stretch with aptitude 0.8.4-1.
In my case it can be reproduced even simpler:
1. Install some package which has a dependency with apt-get, for example:
$ apt-get install apt-src
Entry in /var/apt/history.log:
Start-Date: 2017-01-31 19:51:29
Commandline: apt-get install apt-src
Install: libapt-pkg-perl:amd64 (0.1.30, automatic), apt-src:amd64 (0.25.2)
End-Date: 2017-01-31 19:51:30
Note that package libapt-pkg-perl was installed automatically as a
dependency.
This package is also listed in /var/lib/apt/extended_states (last
changed 2017-01-31 19:51:29):
...
Package: libsdl1.2debian
Architecture: amd64
Auto-Installed: 1
Package: libapt-pkg-perl
Architecture: amd64
Auto-Installed: 1
--EOF--
2. Start aptitude. You don't even need to do anything. Aptitude on its
start overwrites /var/lib/apt/extended_states file, removing the entry
for libapt-pkg-perl package:
File /var/lib/apt/extended_states (last changed 2017-01-31 19:59:35):
...
Package: libsdl1.2debian
Architecture: amd64
Auto-Installed: 1
--EOF--
If there are more than one auto packages installed recently with
apt-get, aptitude removes entries for all of them. So it is not the case
that aptitude removes only the last entry, but all entries which were
installed with apt-get since last aptitude run.
