I have found what I believe to be the problem. If the ecobee thermostat has a power failure, it resets the sensors back to the default room. I recently figured that out when I took it off the wall to clean it and when I put it back on, that night my sensors were reset. I knew they were fine the day before and I was thinking "hmmmm, I wonder...."
The next day I put them back in the right spot, power cycled the ecobee, and sure enough, back to the default room. Not sure if this is an ecobee issue or a limitation for how sensors are implemented via HomeKit, but I would guess this is the issue.