IME, if you don't have them blanketing everything and you WC and change carbon afterward, there generally aren't any issues. I've seen tanks that looked like they were covered in coralline, but then I noticed the masses moving, realizing it was flatworms... I'd siphon all I could before treating in that instance.
I support the natural remedy, though. Mandarin's and many wrasses will pick flatworms and other pests. However, they should not be purchased exclusively for that purpose (and not given other nutrition). Mandarins and wrasses pick throughout the day, so they'll wipe them out, but be sure to feed them other foods, too. If you have a finicky mandarin that doesn't eat frozen and isn't getting enough from the tank, Selcon works as a good additive to food to get them interested. ArctiPods from Reef Nutrition are also generally accepted by everyone in my tanks.