Kelly has messed up big time on 2 occassions
Kelly, one of the most intelligent characters on this show, hasn't messed up much. But when she did, it was big time.
The first time, she messed up by deciding to have sex in space and keeping the baby. Everyone knows that in low gravity, bones and muscles don't have to grow strong enough to support the body's weight, which was true in case of the Sojourner and the Mars stint. Result was that the crew ended up burning through resources, Ed almost died (idk why they couldn't program the lander to fly itself in a suborbital trajectory, would have meant less weight, more speed, and not worrying about needing fuel to land, the lander was toast either ways), and Alex was confined to outer space.
The second time, she decides to hijack the ship to land on Titan despite them realising the stolen data wasn't accurate. Now, fortunately, the landing goes well, but she decides to risk the life of the whole crew just because she thought Ed was too chicken to land on the Moon and on Mars, despite not knowing the full context (Apollo 10 wasn't built to land, the dust storm on Mars hid unknown hills till the last moment). Yes, the choice to not land wasn't entirely rational, but the ship hijack was worse, and it destroyed the commander's confidence.
Plus her being the daughter of a dead Helios shareholder and still being unable to fund science robots in season 4 is weird.