The cookies per click is off by a little less than 1 percent when one has both of the following upgrades:
"Santa's Helpers" "Cookie Egg"
My guess as to the reasoning why it is off is as follows:
Most upgrades add to a static multiplier. For example, two cookie upgrades which each give +5 pp increase together give 1 + .05 + .05 = 1.1 cookie production, assuming no other multiplier effects. Notably, they do not give (1.05)^2 = 1.1025.
However, these two upgrades do multiplicatively stack, instead of adding to a multiplier that buffs CpC. Therefore, when one has both upgrades, they get 1.1^2 = 1.21, or a 21% increase in CpC, and not an increase of 20% as would be the case if they added.
This makes the value of CpC off by 1.21 / 1.2, or about 0.83% lower than the true CpC should be. Adjusting the value given by the optimizer by this term yielded a CpC consistent with my true in-game value.