I have ordered a Misano Red so looked into this a before ordering and is not a problem specific the that colour, Audi's Misano Red has been around for at least 11 years, maybe longer, Audi's have had the odd paint problems on most colours across the range, but red's are no more proned to problems than any other colour from what i have seen, but people are wary having seen faded paint from the 80's / early 90's so blame the colour of the paint for the problems, but when grey (for example) paint flakes its down to bad paint / application not the colour, I was more worried about fading, but they seam to have sorted that out years ago. You still see the odd old vaxhall corsa driving round with a faded pink bonnet so I think it puts people off reds, it was one of first things the mrs said when I said I wanted red, but was reassuring having seen a few older Audi's with Misano dating date as far as 2002 and paint looks really good still, you only have to look on Auto trader at older cars to see it ages as well as any other colour.
If it was more liable to problems Audi would have dropped it by now, as there have been several new versions of all the models across the range in the last decade, so have had many chances to change, but have stuck with it (and have probably improved the paint)
Hope this helps anyone worrying about buying a red car.
The less people that have it, the more unique my will be so don't pick it as all the paint will fall off when you wash it !