A crucial aspect in boundary-coupled problems, such as fluid-structure interaction, pertains to the evaluation of fluxes. In boundary-coupled problems, the flux evaluation appears implicitly in the formulation and consequently, improper flux evaluation can lead to instability. Finite-element approximations of primal and dual problems corresponding to improper formulations can therefore be nonconvergent or display suboptimal convergence rates. In this paper, we consider the main aspects of flux evaluation in finite-element approximations of boundary-coupled problems. Based on a model problem, we consider various formulations and illustrate the implications for corresponding primal and dual problems. In addition, we discuss the extension to free-boundary problems, fluid-structure interaction, and electro-osmosis applications.