CREATE TABLE IF NOT EXISTS fails with table already exists

To avoid outputting anything, test for the table in your php before trying to create the table. For example,

$querycheck='SELECT 1 FROM `USERS`';

$query_result=$dbConnection->query($querycheck);

if ($query_result !== FALSE)
{
 // table exists
} else
{
// table does not exist, create here.
}

Try this

$query = "SELECT ID FROM USERS";
$result = mysqli_query($dbConnection, $query);

if(empty($result)) {
                $query = "CREATE TABLE USERS (
                          ID int(11) AUTO_INCREMENT,
                          EMAIL varchar(255) NOT NULL,
                          PASSWORD varchar(255) NOT NULL,
                          PERMISSION_LEVEL int,
                          APPLICATION_COMPLETED int,
                          APPLICATION_IN_PROGRESS int,
                          PRIMARY KEY  (ID)
                          )";
                $result = mysqli_query($dbConnection, $query);
}

This checks to see if anything is in the table and if it returns NULL you don't have a table.

Also there is no BOOLEAN datatype in mysql, you should INT and just set it to 1 or 0 when inserting into the table. You also don't need single quotes around everything, just when you are hardcoding data into the query.

Like this...

$query = "INSERT INTO USERS (EMAIL, PASSWORD, PERMISSION_LEVEL, APPLICATION_COMPLETED, APPLICATION_IN_PROGRESS) VALUES ('[email protected]', 'fjsdfbsjkbgs', 0, 0, 0)";