A common theme with the tricky methods questions (almost invariably contained in exam 2) is that they are either:
-worded pseudo-ambiguously (I remember that there was a probability question some year back that 4% of the state got right, despite the fact that the maths required was nothing more than plugging something into your calculator; pretty much everyone just misinterpreted it);
-or, as others have mentioned, are really abstract to the point of not even really fitting into a particular topic or section of the course. They might have something to do with, for example, tangents (a core part of the study design), but the hard part is generally a) understanding what the heck is actually going on and b) performing some sort of algebraic manipulation to get the answer you need. The final questions (Q4 and Q5 respectively) of the 2013 and 2014 exam 2s are perfect examples of this.
It also feels like there's a lot more reading in Methods Exam 2 than Spesh Exam 2 (the questions, especially prob ones, tend to be pretty long winded; Tasmania Jones' exploits are generally very detailed :p), which not only puts on more time pressure but increases the chance of misinterpeting what the question actually wants you to find. It feels like a bit of a reading comprehension test sometimes, compared to spesh which is generally more to the point. That also adds to the difficulty of the Methods Exam 2.