Two of them, actually: 1) My understanding is that rest energy, as an invariant, is an "absolute" or "fixed" quantity. Everyone agrees on "how much" there is. But I'm also accustomed to thinking of potential energy as a quantity without a fixed value, so that we only care about the difference in potential energy between two different configurations. Since potential energy within a system contributes to the system's rest energy, something's got to give here, right? Does the mass defect allow us to assign "fixed" value to potential energy, too? 2) If binding energy is negative,* then why is it said that some 99% of the rest energy of a proton comes from the kinetic and potential energies associated with its constituent quarks (with the rest energies of the quarks contributing only about 1%)? Wouldn't the strong nuclear potential energy associated with the quarks decrease the proton's rest energy? *Or if you prefer the convention that calls binding energy positive, read this as "If binding energy must be subtracted to calculate a bound system's rest energy ..."