Aptitude may be the cause of this. I'm not using any other package
manager.
Here is a screen shot. In it, you can see several libraries, which I
have previously marked as automatically installed.
And they are now marked manually installed.
** Changed in: aptitude (Ubuntu)
Status: Invalid => New
** Attachment added: "screen shot"
https://bugs.launchpad.net/ubuntu/+source/aptitude/+bug/1479315/+attachment/4437283/+files/Screenshot_2015-07-31_13-03-00.png
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https://bugs.launchpad.net/bugs/1479315
Title:
Automatically-installed packages are being marked as manually
installed
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