Just because the local jurisdiction has approved your drawings, structural calculations and has issued the building permit does not mean you are out of the woods yet.
If the plan reviewer overlooked something on your drawings that does not meet the requirements of the currently adopted building codes the building department can force you to change the items even though they may already be installed.
Even when an inspector approves a portion of the project you can still be forced to change it to meet the proper life-safety requirements of the code.
Just as the jurisdiction must refund your fees if you are overcharged, they can also require you to pay additional fees if a mistake was made in computing the charges for the permit.