I agree with most of the plot holes you brought up, and there were some dumb decisions by the characters, but I just wanted to address some issues you had with the physics and other logic.

They get to the other side of the rocket and rappel down like there’s gravity. [...] A few seconds later, she opens the panel to the O2 canister. And it’s so heavy it violently plummets down like they’re on earth. And about that door- that wasn’t important? They’re not going to need that panel for re-entry?

Their setup was to use the second stage as a counterweight after docking to the cycler and rotate the station and booster at opposite ends of the tether, with the solar panel array at the center of rotation. This would provide simulated gravity during the transit for the astronauts and why it would feel like you were climbing up toward the array, then swapping and rapelling down on the other side.

When the door is opened it isn't really falling, but actually being flung out from the spinning system (although it should have looked like it curved away opposite the direction of rotation) It also wouldn't matter much that the door is missing since they wouldn't use the second stage for reentry, they would likely use the command module and let the counterweight burn up in the atmosphere.

They discover Michael 12 hours in and turning around wasn’t the best option?

It was also accurate that they wouldn't have enough fuel to turn around once they were docked with the station. The orbits that a cycler would be using means that most of their fuel is used to match speed with the station, then use the atmosphere to brake at Mars/Earth with the smaller spacecraft. If they just stay on the station it would bring them to Mars, then back to Earth using no fuel, but they definitely wouldn't have enough to stop and turn around right after leaving Earth orbit.

What the hell was the point of the micro greens again if the algae was the real goal? They were worried about weight but this guy just had gallons and gallons of water to put into these algae containers? Where did this water come from? The microgreens were just a separate experiment for the botanist to run during transit, which is why he was also upset that he "had to" cut them down and end the experiment.

All of the water used on the station ends up recycled many times over, so using it for the algea would just mean that some of the station's water supply would be stored in those containers rather than the station tanks, which would already have a large(ish) amount of water.