After a level is completed, if there are two Upgrade prompts (each with 3 choices) to dismiss, the controller only works with the first prompt. The second prompt can only be dismissed by using the mouse. I've noticed this bug while using an Xbox 360 controller.

It looks like prompt where you get the 3 choices is called the "NanoCart."

Here is a screenshot of the bug. Basically the bug occurs if one gets two NanoCarts in one level. There is no way to advance to the next screen without using the mouse.