As experienced web developer what is the cause of this issue?

When PHP processes a file, it just outputs lines outside the PHP tags.
So in your sample code, the empty line between the PHP tags is output.

Code:

$ cat test.php
<?php

?>
// This line
<?php

?>

Code:

$ php test.php
// This line
$

Code:

$ cat test.php
<?php

?>

<?php

?>

Code:

$ php test.php

$

Code:

$ cat test.php
<?php

?>
<?php

?>

Code:

$ php test.php
$

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