There is a dog aboard the ship. She is never harmed onscreen, but several outcomes result in everyone on the ship dying. Her death is very lightly implied.
The Captain jumps out of the airlock multiple times during the time loops, and even though we know and they know they will reset back in their cryopod.. kinda fucked up
The whole thing is based around a "loop" in which the two main characters (Mark and the viewer character) die repeatedly. Other major characters also die/are implied to be dead
It can be implied that the Head Engineer is tortured psychologically while stuck in an endless time loop of dying and respawning to build the warp core, if you include the facts there were no ways out of the room, meaning he may have died through dehydration or starving.
The POV character attempts suicide several times (at the start of "Go into the Light..." and every time "Fix it from the Outside!" is selected) but they are always brought back to life.
There are several large robotic characters with masculine voices. They all appear to be part of the same species, and at least one uses she/her pronouns. She is misgendered, though the offender swiftly apologises.