The reason of your problem is the newline character. It is considered a part of the line you read in, but it is not present on the last line in each file. Therefore, '121' plus newline is not the same as '121' without a newline.

Use chomp to get rid of newlines: 

while (my $line = <FILE>) {
    chomp $line;
    # ...

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In reply to Re: ignore duplicates and show unique values between 2 text files by choroba
in thread ignore duplicates and show unique values between 2 text files by perlnoobster

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