As far as I can see, both the command line opening (parse_texi_file in Texinfo/Parser.pm) and include file opening ($command eq 'include' case in _end_line, also in Parser.pm) just call Perl's open. No differing (or special) arguments.
The main difference is that the include file opening has to find the include file, which means splitting apart and putting together the file name path, done in locate_include_file in Texinfo/Common.pm. Your message was happening because that function returned undef, looks like to me. So if the problem happens again, you could put debugging stuff in that function to see why it was failing. Else I see nothing to do ... K
