That's because an auto increment is a independent property of your table, that is only used when assigning new IDs and does not depend on the last existent ID on your table. This is how many relational databases, not only MySQL, were designed for.
To achieve what you want (which seems to be having IDs in sequence without "holes") you would need to query the last ID and increment on it to be set manually.
Ex:
SELECT id from Users ORDER BY id DESC LIMIT 1
Or instead setting the auto_increment of your table according to your last id.
Be aware that both of this is not performatically wise. You should really stick to the auto increment default behavior, since it's optimal, unless you have some strong reason for not doing things as they were designed to be done.