I have the APT_CONFIG environment variable set to pull in an
additional configuration file for apt-get.  Since that file doesn't
exist in pbuilder/cowbuilder environments, it complains like this:

W: Unable to read /home/peter/.apt.conf - RealFileExists (2: No such file or directory)

I don't think it causes any real problems, and I have worked around
the issue by adding

unset APT_CONFIG

to .pbuilderrc.  But perhaps pbuilder should do that itself.