My USB or StiQ has new folders called Spotlight v100 and Trashes

These folders are created by Apple or Mac computers and put onto USB drives as an organizational addition. They are not viruses. Although they are not part of the Intelliquilter software, they will not interfere with anything. If you regularly use an Apple or Mac computer, go ahead and leave the folders on the USB. If you usually use another type of computer, you can go ahead and delete them to free up some space.