Assassin's Creed II/Headscratchers

Sun Fail

 * So there I was, standing on the wall of Monterrigioni, waiting for the sun to rise. And as I watched, the full moon, slowly, majestically, sunk towards the horizon, touched it, and disappeared. And then, the sun rose from the spot it had vanished.
 * Doesn't the moon set in the east? *does research* Ah, yeah....good point...

Bang Bang

 * The gun. I agree with Yahtzee. Yes, it's incredibly pimpy to headshot people, but could the technology of the day really deliver a wrist-mounted micro-musket?
 * What Yahtzee forgot is that it isn't just the "technology of the day". It's knowledge gained from the Apple of Eden itself. Altair pulled the design out of the Apple, wrote it down, and built it. Shazam, wrist-mounted micro-musket made.
 * Remember, Yahtzee has never been terribly good at following the plot and in-game information of any story he's experiencing (for pity's sake, he had trouble following Black Ops' story) so he's not likely to catch something like an optional codex page that explicitly spells out how Altair engineered the gun.
 * Also, clockpunk. Clockpunk needed.
 * And furthermore, it takes a day and a night to set up the shot as it is. Sure, it kills in one hit, but it takes a good five seconds for the shot to be completely lined up for accuracy.
 * Also keep in mind that the fourth glyph all but outright says that firearms were never invented by mankind, and that gunpowder itself was created using a Piece of Eden. Revelations implies that Altair engineered the actual first firearm using the Piece of Eden to provide him with the schematics.
 * It's a video game, who cares?

Romagna Marsh

 * How the hell did Caterina Sforza (who can't swim) get stranded on a rock in the middle of a marsh?
 * If the rest of the area is anything to go by, the tides tend to vary greatly in Romagna (hence the flooded buildings near the coast). Maybe Caterina got up on that rock to read a book or watch the ships come in or take a nap or something and got stuck there when the high tide rolled in.
 * In the novel, she and her husband were out in a boat and she was yelling at him about something he did, so he lost his temper and abandoned her on the rock.
 * Which kinda explains why she had him killed.

Post Game

 * During the game, Medici is declared to be dead yet after the game contracts it's still possible to kill guards wishing to kill Medici.
 * Lorenzo may be dead, but Medici family members are still around and still in control of Florence.
 * Also, are the Assassination missions not just memories of Ezio's that you don't play in chronological synchronisation with the plot? You're accessing memories of Ezio's assassinations that he could have completed way before he went to Venice, for example, but since they only add to your overall synchronisation with him, rather than being the meat of it, you can do them whenever.
 * Gameplay and Story Segregation
 * How is it that all the codex pages written by Altaïr in 13th century Syria end up spread around renaissance Italy? Same goes for his armor and the tombs of six random assassins.
 * Revelations reveals that both the Codex pages and the Keys Altaïr carried were passed off to the Polo brothers. Unfortunately for them, the Codex pages ended up getting stolen by the Mongols, and never properly recovered. It's fairly easy to assume that from that point on, the Templars and Assassins were both scrambling to collect them, even if they had little use for them without Eagle Vision. This is why you find some pages around Mario's house and most locked up under Templar guard; the Codex had been so messed up after trading hands so many times that all the pages might as well have been scattered to the wind.

Minstrels

 * Apart from holding the coveted title of Most Irritating Sons Of Bitches On The Face Of The Planet, they seem to legitimately sing in English, because they occasionally sing a verse in English and finish it with a word in Italian that rhymes with the English word. You could explain this away as part of the Animus 2.0 compensating but I don't think it has - in its large, large list of Headscracher-defeating features - a 'Turn Minstrel's Songs Into English Versions Of The Song With The Occasional Italian Word That Doesn't Break The Rhyme Of The Song' setting.
 * I like to pretend the Minstrels were a practical joke by Rebecca. She finished programming the Animus with time to spare so, just to be a smartass, she coded in a bunch of annoying Minstrels complete with annoying makes-no-sense songs.

Desmonds Running animation

 * So what's the deal with the fact that Desmonds free-running animations completely change from Assassin's Creed 2 to Brotherhood. In the training in 2 he has a much more loose and bouncy style that doesn't use his hands as much where as in brotherhood they seem to have just copy and pasted Ezio's
 * The bleeding effect?
 * Yes, it's the bleeding effect. The whole point is that Desmond picks up Ezio's skills. The fact that he starts running exactly like Ezio means that the bleeding effect is having exactly the effect that the Assassins want on Desmond.
 * Actually after looking closer, his free-running in Brotherhood is closer to Altair's then Ezio's, he lacks the hand over hand climbing and the big jumps that Ezio can perform.

Subtitles

 * If the subtitles are only available on Animus 2.0, how are there subtitles when you're in the Animus 1.0 and Ezio is born?
 * No one said that the original didn't have subtitles.
 * Except Desmond says the subtitles were a "huge plus", and there were no subtitles options in the Animus 1.0.
 * That was a reference to the Animus sequences being in English with the occasional foreign word - the subtitles translate the non-English, which is useful for the viewer.