id='selectmin' you are creating 5 identical HTML block with the same id? ID are unique and only gonna select the first match that's why it only show once.
Use 'selectmin$i' so it create a unique id for each loop:
<?php
$i = 0;
while($i < 5){
$i++;
echo "<input type = 'hidden' id = 'minute$i' value = ''>
<input type = 'hidden' id = 'second' value = ''>
<br><br>
<span id = 'selectmin$i' value = '0'></span>:<span id = 'selectsec$i' value = '0'></span>
<br><br>";
echo "<script>document.getElementById('selectmin$i').innerHTML = 'Hello '; </script>";
}
?>
Also close your while loop with } and use <?php or <? to start your php code.
The output HTML is:
<input type='hidden' id='minute1' value=''>
<input type='hidden' id='second' value=''>
<br>
<br>
<span id='selectmin1' value='0'></span>:<span id='selectsec1' value='0'></span>
<br>
<br>
<script>
document.getElementById('selectmin1').innerHTML = 'Hello ';
</script>
<input type='hidden' id='minute2' value=''>
<input type='hidden' id='second' value=''>
<br>
<br>
<span id='selectmin2' value='0'></span>:<span id='selectsec2' value='0'></span>
<br>
<br>
<script>
document.getElementById('selectmin2').innerHTML = 'Hello ';
</script>
<input type='hidden' id='minute3' value=''>
<input type='hidden' id='second' value=''>
<br>
<br>
<span id='selectmin3' value='0'></span>:<span id='selectsec3' value='0'></span>
<br>
<br>
<script>
document.getElementById('selectmin3').innerHTML = 'Hello ';
</script>
<input type='hidden' id='minute4' value=''>
<input type='hidden' id='second' value=''>
<br>
<br>
<span id='selectmin4' value='0'></span>:<span id='selectsec4' value='0'></span>
<br>
<br>
<script>
document.getElementById('selectmin4').innerHTML = 'Hello ';
</script>
<input type='hidden' id='minute5' value=''>
<input type='hidden' id='second' value=''>
<br>
<br>
<span id='selectmin5' value='0'></span>:<span id='selectsec5' value='0'></span>
<br>
<br>
<script>
document.getElementById('selectmin5').innerHTML = 'Hello ';
</script>
}on yourwhileloop.document.getElementById('selectmin').innerHTML = 'Hello ';<?Javascript echo '<script>alert(phpinfo());</script>'; ?> //confusedphpinfowould need to be a global JavaScript variable to be used there