I've found that the issue was caused by the Catchfile package. It added quoted
file to the list of used files. I've added fix for that.
Is there a problem in the catchfile package itself?
At a first glance I didn't see a place where it would add quotes.
It uses the following macro:
\def\CatchFile@CheckFileExists#1{%
\IfFileExists{#1}{%
\expandafter\CatchFile@DefFile\@filef@und\@nil
\begingroup\expandafter\expandafter\expandafter\endgroup
\expandafter\ifx\csname @addtofilelist\endcsname\relax
\else
\@addtofilelist\CatchFile@File
\fi
}{%
\let\CatchFile@File\relax
}%
}%
The quotes are added in \filef@und, which is set by \IfFileExists.
Best regards,
Michal