One was one on media as a plural noun. (Trapped just about everyone. The only ones who got it right were previous students of mine.)
The second was on affect v. effect.
Each term nearly all the students got it wrong.
Grammar Girl had a wonderful posting on the differences: Effect Versus Affect
The sad part is that even after hammering on the differences for the whole term, in the final quiz, about 1/3 of the students STILL don't understand the difference. (Oh well, you can lead a horse to water...)
BTW, I strongly recommend assigning Grammar Girl as part of the official reading list. She has a weekly short column, which is also done as a podcast. (That way the students can listen to the lesson at their leisure.)
And she does it all with a sense of humor normally missing from grammar nazis.