If you're worried about the appearance, then get them fixed...the rubber coating is just for looks.
Mine have been like that almost since day one...going on my 3rd season with them and they look like they've been through battle...still waterproof (stepped in a creek earlier this year and dry as a bone).
ditto, mine look ruff on the toe but still work.
as for how it happens like someone asked, i know the first couple was my fault cuz one morning before a ride i wasnt thinkin and kicked the bottom of the running board to break up the ice. as for the rest of the nicks i couldn't tell ya, they just showed up.