We study the impact of nonrenormalizable operators in flipped SU(5) that can generate a large? term, R-parity violation, and rapid proton decay. While our motivation is to determine whether F-theory can naturally realize flipped SU(5), this analysis is general and leads to a characterization of symmetries capable of controlling such operators and should be independent of F-theory. We then discuss some specific implications for Ftheory model building, where a significant ? problem is unavoidable. Finally, we mention previously noted difficulties associated to engineering GUT-Higgs fields in F-theory, suggest a direct engineering of SU(5)×U(1)χ as an alternative, and present a sample construction of this type.