If you experience this issue, you are likely utilising Kounta's Option Sets.
And because Option Sets are based on the underlying Products/Modifiers, it is important to ensure that both are set to the same price.
Looking at the "Lactose-free milk" example below, if we want to charge 50c for this then both the Product and the Option Set Option need to be 50c:
Note that you should not need to synchronise your menu from Kounta again.