Tactful way to discuss an error in a published paper
Use neutral and respectful language, but don't beat about the bush. If the model is wrong, say so. And remember to attack the idea, not the person.

Perhaps say something like:

"This work determined that the while the assumption that [quantity] is conserved is correct in the simpler case of model 1, this does not appear to be correct for the more complex case presented in model 2. This was established by [details of work that lead you to this conclusion]. It was instead found that the quantity is determined by [formula]. Model 2 therefore needs to be amended to [something]."

(I'm not sure if I've quite met all the requirements I've listed, but hopefully it'll give you something to go on.)