I added "warn $self->filename" to "sub filename_without_inc" in Devel::NYTProf::FileInfo:

sub filename_without_inc {
    my $self = shift;
    my $f    = [$self->filename];
warn $self->filename;

These warnings lead me to believe the problem is not in my code:

Reading nytprof.out
Processing nytprof.out data

collapse_sibling_evals: nested evals in (eval 656)[/ExtUtils/MM_Unix.pm:2920] 
not handled at /Devel/NYTProf/FileInfo.pm line 291.

collapse_sibling_evals: nested evals in (eval 2695)[/Module/Metadata.pm:13] 
not handled at /Devel/NYTProf/FileInfo.pm line 291.

Here are the results with my added warn:

98% ... (eval 657)[(eval 656)[/ExtUtils/MM_Unix.pm:2920]:1] at /Devel/
+NYTProf/FileInfo.pm line 431.
(eval 657)[(eval 656)[/ExtUtils/MM_Unix.pm:2920]:1] at /Devel/NYTProf/
+FileInfo.pm line 431.
Warning: something's wrong at /Devel/NYTProf/FileInfo.pm line 431.

99% ... (eval 2699)[(eval 2698)[/Module/Metadata.pm:13]:6] at /Devel/N
+YTProf/FileInfo.pm line 431.
(eval 2699)[(eval 2698)[/Module/Metadata.pm:13]:6] at /Devel/NYTProf/F
+ileInfo.pm line 431.
Warning: something's wrong at /Devel/NYTProf/FileInfo.pm line 431.
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Here's line 13 of Module::Metadata:

sub __clean_eval { eval $_[0] }

Here's line 2921 of ExtUtils::MM_Unix (right after strict is disabled on line 2917, and warnings are disabled on line 2919):

eval($line); ## no critic