auto increment primary leaving gaps in counting

You can create a trigger to handle the auto increment as:

CREATE DEFINER=`root`@`localhost` TRIGGER `mytable_before_insert` BEFORE INSERT ON `mytable` FOR EACH ROW 
BEGIN
  SET NEW.id = (SELECT IFNULL(MAX(id), 0) + 1 FROM mytable);;
END

This is by design and will always happen.

Why?

Let's take 2 overlapping transaction that are doing INSERTs

• Transaction 1 does an INSERT, gets the value (let's say 42), does more work
• Transaction 2 does an INSERT, gets the value 43, does more work

Then

• Transaction 1 fails. Rolls back. 42 stays unused
• Transaction 2 completes with 43

If consecutive values were guaranteed, every transaction would have to happen one after the other. Not very scalable.

Also see Do Inserted Records Always Receive Contiguous Identity Values (SQL Server but same principle applies)