Do you think this house may have had more than it’s fair share of noxious gases, CO and maybe even embers entering into it? The first photo is obvious, the water heater flue is not connected to the draft hood and all the burnt gases are entering the water heater closet which is open at the top into the attic. The second photo is not quite as obvious. It’s looking up into the throat of the fireplace firebox, you can see the double wall pipe is not lined up with nor connected to the firebox collar. Gases, embers, etc can & will escape into the wooden chimney chase. How did this home not kill someone or burn down after 15 years?
Was the roof recently replaced? I’ve found this problem many times after a re-roofing. The roofers don’t check to verify if the vent pipes are realigned with their respective furnaces or water heaters.
Yes, about 24 months ago! Good call, that could certainly explain the WH but not the chimney.