I had a similar problem with my first Jazz (2004 se auto) in the pedal area but not a place where you would rest your foot, the dealer took photos to send to Honda and they replaced the carpet under warranty, this occurred in the first year of ownership but the problem never reoccurred in the following 3 years of ownership, so it must have been a manufacturing problem so keep on at your dealership to sort it out. 
Good to know ! I will be going to Honda Direct but have sent the images to a vehicle trimmer who can do a 'repair' of sorts for £35... he will make up his mind how to tackle it when he sees it on the flesh. (Not the photos) Also not sure how it will look...I really do think I had a defective carpet
How unlucky is that!
