The current edition, WFRP 4E. Here are a few reasons for our confusion and things that just seem not intuitive or that slow down gameplay as we try to figure out things.
1) 4 pools of expendable points that are all very similar, named similarly (fortune, fate, resilience, and [some other r-term I've forgotten])
2) keeping track of advantage points for characters and every enemy
3) hit locations, figured out by flipping the die roll (just a confusing extra step)
4) critical hit and miss charts
5) lingering wound charts
6) counting success levels by subtracting die rolls and comparing to the die roll of another person
7) adding success levels based on ranks of talents
8) several "special die roll"combinations that give different results (criticals, failures, spell mishaps all have different combinations)
9) advancing characters is confusing, spending XP at different rates
These are just the first few that come to mind. I'm concerned that the rules are so complicated that I won't be able to focus on the plot, mystery, characterization, roleplay, or anything else but run the game as a wargaming simulation.