Magnetic fields and mass accretion processes create cold and hot spots on the surface of young stars, which affect the global temperatures measured on the sources. Previous studies have reported this problem on individual stars, but none has performed a large-scale study on this subject. We present an iSHELL K-band survey of 40 Classical T Tauri stars in Taurus and Ophiuchus, which aims to investigate the effects of starspots on the surface of young stars. We combined our infrared observations with optical measurements and found significant temperature differences between optical and IR values. The measured temperature differences increase with stellar temperature but also with magnetic field strength. To further understand the effects of the spots, we analyzed a sub-sample of 25 stars that have dynamical masses measured with ALMA. Using evolutionary models, we computed stellar masses from both optical and IR temperatures and compared them to the ALMA derived masses. In the range of stellar masses analyzed here (0.1-1.2 solar masses), we found that, on average, the IR temperatures are better indicators of the stellar masses than the optical temperatures. This result could indicate that hot spots skew the optical temperatures of the stars, and thus optically derived masses are higher than they should be.