As has been stated, the line between NDL dives and dives that have slight deco obligations is very easily blurred; different computer algorithms, different physiology, etc...that's why we have safety stops. They add a margin of safety, and it is impressive how much N2 is off gassed during a brief shallow stop; something like close to 90% on NDL profiles. (I think I read that in the PADI encyclopedia)
I almost always do longer safety stops than 3 minutes; I have found that it makes me feel better when doing multiple dives/day, particularly on air. If I miss one accidentally, it's because there is some problem on the dive that has likewise increased my ascent rate. This has happened to me when guiding new divers that have poor buoyancy control. In those cases I have gone back down and done as long a stop as is practical. I'd be interested in learning more about possible dangers with this practice.
However, with a new diver who has possibly had all sorts of problems on a dive, including missing a recommended safety stop, I would be much more hesitant to send (or bring) this diver into the water for a stop. I'd be more likely to closely monitor for signs of DCS and possibly put the diver on O2.