No spoilers for the sequels, please. Thanks! 
1. If the Company knew about the signal and deliberately sent the Nostromo into its vicinity, why did it allow the computer to (possibly) identify the signal as a warning? (Though that was a cool beat; I'll give it that.)
2. How did the cat get in that storage box? How did the motion sensor pick it up through what looked like a pretty well-sealed door? And why, minutes after ordering everyone to travel in pairs, does Ripley let the hat-wearing dude wander off for several minutes, when it becomes clear that finding the cat wasn't a piece of cake?
3. The captain screwed up his own plan pretty well, didn't he? There was no reason to believe the alien knew about his flame-thrower or had any cause to fear him, so as long as he stayed put, he had the upper hand. But a bit of Lambert screaming rattles him enough to move down a freakin' ladder, which negates his entire weapon ability?
4. For that matter, the flame-throwers were admittedly cool, but on a ship with that much metal and gear, wouldn't there be some heavier-duty potential weapons? If not guns or laser guns, laser cutters or at least arc welders?
5. I suppose the Company assumed that the alien won't have any interest in Ash, and that he'll be able to pilot the ship home? A dubious assumption, seeing as he's been eating and hanging around with the human-scented crew, but okay, I'll bite...
6. How can Ripley be so close to the alien in the shuttle and not smell it? Does it really not smell like anything? Has she no sense of smell? (Seems this scene was an unscripted one by Scott... out-universe, that makes sense...)
Don't get me wrong; I enjoyed the movie, and a homicidal alien is at least more plausible than Jaws' ship-destroying shark (riiiiggghhht), and then I suppose horror movies require characters to act stupidly, but...

1. If the Company knew about the signal and deliberately sent the Nostromo into its vicinity, why did it allow the computer to (possibly) identify the signal as a warning? (Though that was a cool beat; I'll give it that.)
2. How did the cat get in that storage box? How did the motion sensor pick it up through what looked like a pretty well-sealed door? And why, minutes after ordering everyone to travel in pairs, does Ripley let the hat-wearing dude wander off for several minutes, when it becomes clear that finding the cat wasn't a piece of cake?
3. The captain screwed up his own plan pretty well, didn't he? There was no reason to believe the alien knew about his flame-thrower or had any cause to fear him, so as long as he stayed put, he had the upper hand. But a bit of Lambert screaming rattles him enough to move down a freakin' ladder, which negates his entire weapon ability?
4. For that matter, the flame-throwers were admittedly cool, but on a ship with that much metal and gear, wouldn't there be some heavier-duty potential weapons? If not guns or laser guns, laser cutters or at least arc welders?
5. I suppose the Company assumed that the alien won't have any interest in Ash, and that he'll be able to pilot the ship home? A dubious assumption, seeing as he's been eating and hanging around with the human-scented crew, but okay, I'll bite...
6. How can Ripley be so close to the alien in the shuttle and not smell it? Does it really not smell like anything? Has she no sense of smell? (Seems this scene was an unscripted one by Scott... out-universe, that makes sense...)
Don't get me wrong; I enjoyed the movie, and a homicidal alien is at least more plausible than Jaws' ship-destroying shark (riiiiggghhht), and then I suppose horror movies require characters to act stupidly, but...
