There are a couple of different possibilities.
With E&M, you tend to lose the intuition you could rely on with mechanics. You probably have a good feeling for what 10 meters is, but what is exactly is 10 V? Resistance kind of makes sense, but what are capacitance and inductance?
Mathematics. (1) Vectors will make their appearance again. (2) Not only do vectors appear but the concept of vector fields does as well. (3) Applying the ideas of vector calculus to problems throws many students. (4) RC, RL, and RLC circuits are described by differential equations, which some find confusing. For many students, they're essentially learning physics and the necessary mathematics concurrently.
Recognizing and taking advantages of symmetry seems to be a problem for some students. The problems are much simpler if you use symmetry, but you can't do that unless you see it's there.
Seeing the big picture. It's easy to get lost in a zoo of formulas in intro E&M. If you see how everything is related, though, it can bring order to the apparent chaos. A lot of students, however, aren't terribly interested in learning where a formula comes from.
Magnetism is inherently three-dimensional because it involves cross products. Some people struggle with visualizing situations in three dimensions.