When there is a source file in the top-level directory of a project (one of the directories passed with --prefix), the die("file error for " ...) call gets triggered: @$short_path has only one element, so nothing gets passed to File::Spec->catdir() and $rel_dir is empty.
Adding unshift @$short_path, '.' if $#$short_path == 0; before the call to catdir() avoids the crash but generates an HTML coverage report with no way to access the source files because the top-level directory has a zero-length (or no?) hyperlink to the per-directory report file.
With lcov 1.16, this would give the name "root" to the top-level directory.