I think Apple broke something with iOS 12 and HomeKit. Ever since updating, my smart thermostat (Honeywell Lyric T5, bought specifically to use with HomeKit) will randomly show "Not Responding" in the Home app, despite it not losing it's connectivity nor functionality (I can still change it's settings through the Honeywell app). Weird thing is the Home app on my MacBook will show the same status. But it will randomly clear itself up and display/work normally within the Home app.
Never had this issue on iOS 11, it was flawless. It's not a huge deal as I usually only change the temp during season changes and leave it on the same temp the whole season (the way heat pump systems are designed to run). 12.1 nor macOS 10.14.1 did anything to fix this, as I noticed it this morning on both. But willing to bet I can give it an hour or so, check the app, and it will be responding normally.
In googling around, this seems to be a common issue with HomeKit, though others have experienced issues before iOS 12. That's just when I noticed it starting to do this.