The rational design principles established for metal-organic frameworks (MOFs) allow clear structure-property relationships, fueling expansive growth for energy storage and conversion, catalysis, and beyond. However, these design principles are based on the assumption of compositional and structural rigidity, as measured crystallographically. Such idealization of MOF structures overlooks subtle chemical aspects that can lead to departures from structure-based chemical intuition. In this Perspective, we identify unexpected behavior of MOFs through literature examples. Based on this analysis, we conclude that departures from ideality are not uncommon. Whereas linker topology and metal coordination geometry are useful starting points for understanding MOF properties, we anticipate that deviations from the idealized crystal representation will be necessary to explain important and unexpected behaviors. Although this realization reinforces the notion that MOFs are highly complex materials, it should also stimulate a broader reexamination of the literature to identify corollaries to existing design rules and reveal new structure-property relationships.