Because in the first case you are still inside the loop when you print the array @out, and in the second case you reassign to the array @arr1 each time through the loop.

Update: try this (untested):

my @wanted;
for my $line ( @lines ) {
    my @fields = split /,/, $line;
    if ( $fields[2] eq '1' || $fields[2] eq '0' ) {
        push @wanted, $fields[4];
    }
}
@wanted = uniq @wanted;
print "$_\n" for @wanted;
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Hope this helps!