We report unusual absolute negative resistance phenomena in twisted superconducting yarns consisting of niobium-nitride (NbN) nanowires formed on a template of aligned carbon nanotube (CNT) sheets. In the vicinity of the superconducting critical temperature and critical current, the electrical resistance with a standard four-probe configuration exhibits negative values for many wire-shaped twisted yarns. This anomalous behavior at the superconducting transition stage is analyzed using a simplified circuit model, where the charge conduction is determined by the combination between the intra- and internanofiber transports inside the yarn. The superconducting transition of intrafibrillar transport along CNT-templated NbN nanowires was distinguished from that of an interfibrillar one, where the latter exhibits the ensemble property of superconducting weak links among adjacent NbN nanowires. Furthermore, the topological similarity between the sheet of an aligned array of nanowires and the yarn of twisted nanofibrils enables the occurrence of this anomaly. This study indicates that the quantitative network-based approach is effective for the analysis of anomalous charge conduction through nanowire-based anisotropic materials.