How does magic work if all things are dependently originated?

With the view of dependent origination, we see that things happen due to conditions. There are even certain laws that can be expressed regarding the various mechanisms of causation (i.e. gravity, electromagnetism, etc.), although the word causation is a sticky one because there is never one cause for anything, and the laws themselves are ultimately unexplainable except that we observe them functioning (i.e. we must assume that "somehow" the electromagnetic force exists). 

The most obvious question that people have when first considering the idea of universal laws, is something like this: how is it that the universe has laws if yogis are able to break all laws of nature with the power of their minds?

I could come up with some hypothesis of how yogic powers are able to "alter" laws of nature or what we perceive as altering, but it wouldn't be worth my time. First, let me note that pretty much every yogi (even non-buddhist ones) that I've read of has stated that siddhis (spiritual powers) are mere illusion, just tricks, and so it is best not to demonstrate them to folks as it will only confuse them more. It is possible, for example, that Jesus did not really walk on water--maybe it was just a mass hypnotism. But, it's also possible that he exploited some physical law like thixotropy, which most folks don't understand: http://www.dedoimedo.com/physics/cornflour.html

Remember, any technology sufficiently advanced will appear as magic. Hold an iPhone up to Isaac Newton and he might think you have magical powers.

Regardless of the particular explanation we choose for so-called magic, ultimately, we must remember that this "magic" itself happened due to conditions. Conditions like, for example, the yogi desiring to perform the miracle. Why did the yogi desire to do that? You see, so even the magical yogi is not free from conditions (although he may be blissfully unaware of this fact, as are most of us, most of the time).