Rebuilt Engine After Cooling System Failure. Overheated Nine Months Later and Coolant is brown

99 Jeep Wrangler 6 cyl 4.0 Automatic
Spent $2800 on an engine rebuild after it seized from overheating. This included new radiator, thermostat and water heater. After nine months the Jeep overheated going up a long grade on the highway. Pulled off and noticed the coolant puddling under the vehicle was brown. Skip to returning and talking to the mechanic that did the job. My complaint was that they must not have properly flushed the coolant system. Which I assume should have been covered thoroughly since the reason for a rebuild was a cooling system failure. They stated that there was/is material in the engine that didn't come loose during their cleaning of the engine that dislodged over the nine months. That doesn't make sense to me. I would think a good flush would take care of any gunk or debris that might rear it's head anytime soon, especially in as little time as nine months. The mechanic says they will put in a new radiator and return the other under warranty (stated to me as they were doing me a favor) but they are going to charge just over $200 for labor.
Appreciate any insight that you may have on this that may either confirm or refute my thoughts on the matter. Thank you for your time.