Usually you see that when you burn an IMG file onto the flash drive.
You can either delete the partitions manually via disk management which takes ages. Or clear the selected disk (diskpart lists them as disk numbers you can find number in disk management).
In command prompt as administrator you type diskpart then list disk, then select disk X (replace d with number), then type clean and then reinitialise disk in disk management.
This is if you don't need to backup the flash drive.