One of my favorites is this: why didn't Voldemort stick around in the Shrieking Shack to make sure that Snape was dead? As important as it was to good ol' Tommy Riddle to take control of the Elder Wand, shouldn't he have at least waited for, like, five or ten minutes and then checked for a pulse or something? But noooo...instead, as soon as Snape fell to the ground, "blood gushing from the wounds in his neck," You-Know-Who just walked out "without a backward glance."
Seems to me that if Voldemort was a little more detail-oriented, he would have been much more successful. But then if he was, we wouldn't even have a story to begin with.
Now don't get me wrong - for the most part, none of these plot holes or whatever detract from my enjoyment of the books I read, movies I watch, etc. It's part of what makes being a fan so much fun. In fact, most of my nerdiness is reserved for the stuff that I love the most: Harry Potter, Star Wars, etc. (In Episode IV, why did Obi-Wan call Darth Vader "Darth"?)
That being said, I tried really hard to make sure Secret of the Songshell was air-tight. Despite my best efforts, I'm sure there's probably a few things in there that I missed. If you've found anything (and/or have a good answer to my Snape question), I'd love to hear from you, you nerd.