Every single time someone tells David he doesn't matter, and there's a tiny spark of pain in his eyes, especially when the hologram of Weyland, his father figure, says it bluntly. He can be seen as going quietly crazy the whole time depending on your interpretation.
Charlie forcing Vickers to do a Suicide by Cop while Shaw is having a complete screaming hysteric breakdown on the sideline.
Vickers herself looks absolutely horrified by what she's just done, even though she probably just saved the ship from The Virus by killing Charlie. She originally just wanted Charlie to stay outside the ship, but Charlie himself realized it was too late.
Vickers and Shaw watching Janeck's Heroic Sacrifice. They look torn, both about the deaths of their friends and the loss of their last chance at getting home.
Despite the Narm of the moment and her Anti-Hero Substitute tendencies, watching Vickers get crushed can feel quite sad.
The Xenomorphs of all things get their moments. The very reason they kill anything that isn't them is because they were designed to be the very weapons they are. They can't actually help killing everything, it's what they are for. It's simply part of their life cycle, and they have no malice at their core.
