You don't need the last next statement. You code could be like this:

while ($line = <MAIN_FILE1>)
{
    print OUTPUT1 "$filename\n" if (exists($hash1{$entry}));
    print OUTPUT2 "$filename\n" if (exists($hash2{$entry}));
}
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Can't figure out why you are printing in the end of the loop...

Hope this helps.