Man, that was just... that episode was just bad! There was so much wrong with it; it's Doctor Who plus pirates! How d'you screw that up that badly?
Like, right at the start, where Amy pulls a sword and fights off all those pirates; there is, of course, the obvious question as to how she attained the necessary swashbuckling skills to fend off a band of seaward vagabonds, but there was also the more obvious, glaring contradiction of "why didn't they just shoot her!?". Granted, this isn't the only work of fiction where that's come into play [http://tvtropes.org/pmwiki/pmwiki.php/Main/WhyDontYaJustShootHim], but that doesn't change the fact that it doesn't particularly make sense for a gang of pirates to rush the woman with a sword with frickin' brooms when they've just been shown to have handy gunpowder-shooters at their disposal.
And a bit later, when those two pirates got siren'd; they didn't have that much trouble holding Rory back, but when the pirates were walking to their deaths the gang were just like "no, wait, don't... ah, he's gone, never mind." I actually came up with a couple of theories as to why the Doctor let the second one happen:
1. He's actually a far more morally vague character than the series makes him out to be, and he needed him dead so he could do the screwdriver thing on his hat to determine the origins of his foe, or
2. He just really wanted his hat.
Furthermore; when the Doctor suddenly decided "ooh, maybe when she vaporizes people she doesn't actually kill 'em! Let's test this theory out!" Like... what if she did kill 'em? That was an immensely stupid move on his part.
And my final qualm... why is it that everybody else got transported to the hold, but the Doctor, Amy and Barbossa didn't? They got taken not a minute after Rory and the kid, so it wasn't an issue of getting them there taking a long time; it was just a glaring plot hole!
Don't mistake me for a "hater" - hell, I actually enjoyed Love And Monsters - but I've got to say, this is my least favourite episode of Doctor Who in due memory. And I was really looking forward to this one...