The moment when Jake finally remembers exactly what went on inside the alien ship. Particularly disturbing is seeing Jake's girlfriend being vivisected by the alien scientist. Aliens Are Bastardsindeed.
The aliens themselves are full of this, which leads to two extremely effective Jump Scare moments.
The alien scientist, and what he does to Lonergan's lover.
The human captives being hypnotized by the light.
Oh god. LUNG HANDS.
The entire movie. It can give a person a gajillion nightmares.