Defects in a polymer network complicate an accurate calculation of structural parameters such as the molar mass between cross-links Mc, typically obtained from experimental swelling data. In this paper the formation and structure of poly(ethylene glycol) (PEG)-based polyurethane networks containing PEG-mono methyl ether dangling chains are studied. The phantom network model can describe the swelling behavior of these networks only when a composition-dependent interaction parameter is used and the formation of allophanates is accounted for. A clear transition in the network formation is found at the PEG network precursor molar mass at which entanglements are formed in the melt. Correction factors based on structure calculations using the Miller-Macosko-Vallés probability approach are proposed and validated for an accurate calculation of the Mc of these defect-containing networks. This provides a new approach for studies that requires an accurate estimate of the Mc, only based on experimentally straightforward swelling experiments.