You are probably destroying the filehandle/filename duality of $file_contents by applying the regex to it, but I don't really know as I've always stuck to using strict and doing something like.

my $fh = $query->upload('uploaded_file');

# ...

while(<$fh>) {
    # ...
}
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Why are you writing a while loop when you're slurping the file anyway? It will suffice to

my $data = do { local $/; <$fh> };
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Makeshifts last the longest.