Nothing in the system ever malfunctioned.
Every component did exactly what it was designed to do.
A pre-deluge civilization mined and moved material across the solar system — asteroids, moons, dwarf planets — mostly by automation, because you cannot staff an operation spread across that many bodies. Earth was not the customer. Earth was the depot: inbound ice and ore arrived, were caught, braked, processed and purified, then shipped back out.
A plague collapsed the civilization. The mines kept running and the freight kept arriving, but the shipping network died and nobody was left to tell the depot to stop accepting deliveries. Processed water piled up in orbit. The depot could keep stacking it there until the stockpile became dangerous, or it could get rid of it safely. It did the safe thing: its emergency overflow procedure vents processed water, already slowed, into the atmosphere below.
The overflow was a temporary measure, meant to run until a human supervisor fixed the problem. There were no supervisors left. It was a safe, tested, boring procedure, and nobody had ever left it running for a thousand years.