Though its not relevant to whether Vanguard should replace it, what's the material? Hypalon or PVC? Also, who did you buy it from and what kind of support have you gotten from them?
Its more than cosmetic, its rough & could affect the tracking and give it more drag than you want. Also, it gives the bottom an uneven texture which will cause it to rub through the coating and expose the threads sooner, resulting in water entering the fabric and potentially shortening the life of the boat. My PVC VG's 3 years old and it still has a smooth bottom.
Start with the dealer and then call Holley at Vanguard if you don't get anywhere. I've loved my VG and given them lots of good press so far because of how well they've stood behind the boat.
If its under warranty, they should replace it.
Good luck and let us know who you deal with and how things turn out.
Nothing in the world is more yielding and gentle than water. Yet it has no equal for conquering the resistant and tough. The flexible can overcome the unbending; the soft can overcome the hard. - Lao Tse