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Stationary periodic patterns are widespread in natural sciences, ranging from nano-scale electrochemical and amphiphilic systems to mesoscale fluid, chemical and biological media and to macro-scale vegetation and cloud patterns. Their formation is usually due to a primary symmetry breaking of a uniform state to stripes, often followed by secondary instabilities to form zigzag and labyrinthine patterns. These secondary instabilities are well studied under idealized conditions of an infinite domain, however, on finite domains, the situation is more subtle since the unstable modes depend also on boundary conditions. Using two prototypical models, the Swift-Hohenberg equation and the forced complex Ginzburg-Landau equation, we consider bounded domains with no flux boundary conditions transversal to the stripes, and reveal a distinct mixed-mode instability that lies in between the classical zigzag and the Eckhaus lines. This explains the stability of stripes in the mildly zigzag unstable regime, and, after crossing the mixed-mode line, the evolution of zigzag stripes in the bulk of the domain and the formation of defects near the boundaries. The results are of particular importance for problems with large time scale separation, such as bulk-heterojunction deformations in organic photovoltaic and vegetation in semi-arid regions, where early temporal transients may play an important role.