IMO the answer to this question can't be anything to do with quantum mechanics or relativity because few people actually pay attention to subjects like that. If we're going for quantity of misunderstanding rather than quality (and yes I do know that understanding or lack thereof cannot be quantified) I think you need something everyone's actively engaged in and most don't understand. Thus it has to be a very basic principle.
I admit I'm biased but IMO the most misunderstood concept has to be the concept of P=VI. Electrical labels are ubiquitous in our society, we all read them, and the lack of understanding of the basic units of wattage, voltage, and amperage is almost as ubiquitous as the labels themselves. Note I did specifically separate it from Ohm's Law because a lot of folks don't do resistance measurements, but everyone's gone to Home Depot or Lowe's thinking "I need a 55W bulb" without any kind of understanding as to what that actually means.