This is in reference of bug[0] in current master. While I was debugging the code to fix the issue, I found that we are trying to force the column to be primary key if auto_increment has been checked.

there is this comment in Table.class.php:
// Force an auto_increment field to be part of the primary key
            // even if user did not tick the PK box;

anyone have an idea why are we doing so ?

[0] https://sourceforge.net/p/phpmyadmin/bugs/4540/

Thanks and Regards

- Smita