While the comments thus far have been good in having Perl discover your error, I would put forward that there's a human way as well. Whenever I write a function, I always put the following template in:

1 sub foo
2 {
4a    my $self = shift;
4b    my () = @_;
3 }
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The numbers are the order I type the lines in. (4a is used only if I'm writing a method.) By doing this, I guarantee that I have a my () = @_; line. I suspect that if you had had that line in your code, you would've remembered to put the variable in there.

Also, I try very hard to not use the same name in a sub as I would outside the sub. There's a good reason for it, too. In a sub, you're dealing with an abstract flow, so a name like $filename or $fh is useful. Outside, you're dealing with concrete things, so names like $out_filename or $data_fh are much better. So, what you would have is

my $data_fh = IO::File->new($data_filename)
    || die "Cannot open '$data_filename' for reading: $!\n";

my $stuff = read_file_with_format($data_fh);

...

my $second_fh = IO::File->new($second_filename)
    || die "Cannot open '$second_filename' for reading: $!\n";

my $other_stuff = read_file_with_format($second_fh);

...

sub read_file_with_format
{
    my ($fh) = @_;

    ...
}
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------
We are the carpenters and bricklayers of the Information Age.

The idea is a little like C++ templates, except not quite so brain-meltingly complicated. -- TheDamian, Exegesis 6

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.