This is just basically an inconsistency between file() and exec()

file() will return the newline on the end of each element in the array, ie:

$data = file("somefile.txt");

$data[0][ strlen($data[0])-1 ] == "\n"

but exec() doesn't put newlines on it's output:

exec("soemthing", $data); 

$data[0][ strlen($data[0])-1 ] != "\n"

At the least, the manual page for file() and/or exec() should state this behaviour.