Small logic error which you catch after the fact in your output loop.

Assuming unique values in each file, your loops can be reduced to

foreach my $entry (@file1) {
   $index{$entry} = 1
}

foreach my $entry (@file2) {
   $index{$entry} += 2;
}
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Not assuming unique values, to avoid "screwed up" entries, it could be reduced to this

foreach my $entry (@file1) {
   $index{$entry} = 1
}

foreach my $entry (@file2) {
   # '||0' is to still the warnings under 'use warnings'
   $index{$entry} += 2 if (($index{$entry}||0) < 2);
}
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Nothing big.