They covered that towards the end. There are still areas where CIRCLean can be improved. For example, there is an issue open to deal with BadUSB-style attacks,

They covered that towards the end. There are still areas where CIRCLean can be improved. For example, there is an issue open to deal with BadUSB-style attacks, in which a thumb drive mimics another device type (such as a keyboard) with malicious intent. Vinot has indicated one possible solution already: blacklisting all non–mass-storage USB kernel modules. Without USB HID support in the kernel, a malicious drive cannot mimic a keyboard. In an email, Vinot described a few other ideas, such as converting PDFs to the more restrictive PDF/A format before converting them to HTML.