MySQL Workbench auto increment disabled

As a work around, when you click the 'Apply' button and are presented with the generated script to review, you can actually edit that script. I ran into the issue you posted as well and just manually added AUTO_INCREMENT to the column definition I needed it applied to.

You need to set auto increment in table

Just check the AI(Auto Increment) checkbox. No work around, that's why it's a workbench. Life made easy