Transient structures based on associative polymers can deliver complex functions; as such, they hold promise for advanced applications as in drug delivery, tissue engineering, and electronics. The network structure and timescale of its rearrangement are key factors that define their range of utility. However, the inevitable phase separation of polar pairwise associations from nonpolar polymer chains frequently causes junction aggregation, whose stability and functionality significantly affect the network structure and dynamics, and as such, redefine its utility. Engineering the extent of association is a necessity for controlling properties of supramolecular materials, yet the current knowledge of the effect of design parameters on specificities of aggregates and their consequent effects on material properties is limited. To address this gap, the importance of aggregation is highlighted, the available theories and models of the dynamics of associative polymers in the presence of aggregates are reviewed, and the existing experimental records to draw a general guideline for interpreting the effect of aggregates on polymer dynamics are classified. Moreover, pitfalls and considerations like the applicability of time-temperature superposition, and the interplay of kinetics and thermodynamics of aggregation that may undermine the authenticity of the reported data are reviewed.