The only disadvantage I've noticed is when hammering hard and banging gears. Then my feet tend to move around on the pedals. Not dangerously, but I find it mildly annoying.

But flat pedals have advantages too. Riding in any shoes is a big one. I run flats on my road bike all winter, since it means I can wear warmer shoes. Instant, thoughtless foot removal is another advantage. That's why my mountain bikes only run flats... it makes "emergency dismount" more common than "crash".

I'm pretty sure studies have shown little or no performance advantage to clipless, which agrees with my experience. Still, I like them for the secure attachment in some situations. Like fast road rides, or any fixed gear riding.