You're incrementing an element of %seen twice with each pass. That will prevent printing, but @uniq should contain what you expect.

Try this instead:

my @uniq;
my %seen;

for (0 .. $#name1) {
    next if $seen{$name1[$_]}++;
    push @uniq, $name1[$_];
    print "$name1[$_]\t$name2[$_]\t$percent[$_]\n";
}
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