The main one that I remember off hand was specifically about her squid baby. Elizabeth’s squid-fetus, meanwhile, has grown to monstrous proportions despite being locked in a small room with no sources of food or other places for the additional mass to have come from.

I feel like I have to re-watch it now because I know there are other ones.

Also a lot of these little questions. Why did the Engineers show a star-map to their weapon facility instead of their home planet? Why were the Engineers running away from a threat to go inside the cargo room instead of another non-dead-end option? What happened to the other alien ships? Did the threat attack all the alien ships at the same time to make it impossible for one of them to escape? Why was there still one living Engineer inside the spaceship? Wouldn’t the threat kill him too? The alien spaceships have been underground for more than 2000 years; did no one back home want to see what happened? Why did Janek not care at all about the 2 scientists trapped inside the alien cave? What is the purpose of those random pixelated flashbacks of the Engineer crew running? Why was everyone so relaxed about finding out the biggest revelation of human history? And why, oh why was there a goddamn flute to activate the alien ship?

Another thing, I don't think it was so clear cut that they wanted to destroy their own creations because they were scared of what they created. It seems like there is some other reason behind them wanting to exterminate all life. I read an interview where the director said that most of the unanswered questions in the plot will be resolved in the sequel but he likes the way the film leaves certain questions unanswered because he wasn't completely sure if they would be approved for a sequel. The script for it is done though it was completed last year in Oct.