PHP - Php Files With Bom Or Without Bom ?

So far I have managed to create an upload process which uploads a picture, updates the database on file location and then tries to upload the db a 2nd time to update the Thumbnails file location (i tried updating the thumbnails location in one go and for some reason this causes failure)

But the main problem is that it doesn't upload some files

Here is my upload.php

<?php
include 'dbconnect.php';

$statusMsg = '';

$Title = $conn -> real_escape_string($_POST['Title']) ; 
$BodyText = $conn -> real_escape_string($_POST['ThreadBody']) ; 
	 

// File upload path
$targetDir = "upload/";
$fileName = basename($_FILES["file"]["name"]);
$targetFilePath = $targetDir . $fileName;
$fileType = pathinfo($targetFilePath,PATHINFO_EXTENSION);
$Thumbnail = "upload/Thumbnails/'$fileName'";

if(isset($_POST["submit"]) && !empty($_FILES["file"]["name"])){
    // Allow certain file formats
    $allowTypes = array('jpg','png','jpeg','gif','pdf', "webm", "mp4");
    if(in_array($fileType, $allowTypes)){

        // Upload file to server
        if(move_uploaded_file($_FILES["file"]["tmp_name"], $targetFilePath)){

            // Insert image file name into database
            $insert = $conn->query("INSERT into Threads (Title, ThreadBody, filename) VALUES ('$Title', '$BodyText', '$fileName')");
            if($insert){
               $statusMsg = "The file ".$fileName. " has been uploaded successfully."; 

		$targetFilePathArg = escapeshellarg($targetFilePath);
		$output=null;
		$retval=null;
		 //exec("convert $targetFilePathArg -resize 300x200 ./upload/Thumbnails/'$fileName'", $output, $retval);
		 exec("convert $targetFilePathArg -resize 200x200 $Thumbnail", $output, $retval);
		echo "REturned with status $retval and output:\n" ; 
		if ($retval == null) { 
		echo "Retval is null\n" ;
		echo "Thumbnail equals $Thumbnail\n" ; 
		}

            }else{
                $statusMsg = "File upload failed, please try again.";
            } 
        }else{
            $statusMsg = "Sorry, there was an error uploading your file.";
        }
    }else{
        $statusMsg = 'Sorry, only JPG, JPEG, PNG, GIF, mp4, webm & PDF files are allowed to upload.';
    }
}else{
    $statusMsg = 'Please select a file to upload.';
}

//Update SQL db by setting the thumbnail column to equal $Thumbnail
$update = $conn->query("update Threads set thumbnail = '$Thumbnail' where filename = '$fileName'");
            if($update){
               $statusMsg = "Updated the thumbnail to sql correctly.";
		echo $statusMsg ;  } 
else 
{ echo "\n Failed to update Thumbnail. Thumbnail equals $Thumbnail" ; } 


// Display status message
echo $statusMsg;
?>

And this does work on most files however it is not working on a 9.9mb png file  which is named "test.png" I tested on another 3.3 mb gif file and that failed too?

For some reason it returns the following

Updated the thumbnail to sql correctly.Updated the thumbnail to sql correctly.

Whereas on the files it works on it returns

REturned with status 0 and output: Retval is null Thumbnail equals upload/Thumbnails/'rainbow-trh-stache.gif' Failed to update Thumbnail. Thumbnail equals upload/Thumbnails/'rainbow-trh-stache.gif'The file rainbow-trh-stache.gif has been uploaded successfully.

Any idea on why this is?

array:
[SomePath/test.php] = "All In this php file is being read by a new smart function!";
[SomePath/Weird/hello.txt = "Hello world. This is me and im just trying to get some help!";