Stellar activity and variability in Young Stellar Objects (YSOs) influences our ability to accurately constrain both the fundamental stellar parameters and the activity level of the stellar surface, which in turn hamper the characterization of planetary atmospheres. Magnetic fields at the stellar surface can be strong enough to block convection, generating large cool starspots that emit at temperatures colder than the photosphere. Because of this, optical-near infrared spectra of these systems are a complex synthesis of multiple components. In addition to the previously considered stellar photospheres and chromospheres, stellar and disk winds, and circumstellar accretion and disks, a recently recognized component is starspots. Quantifying the spectral contributions from any of these processes requires us to disentangle the complicated multicomponent emission. Here we present results from spectral modeling of sixty accreting and non-accreting YSOs (
$\leq$25 Myr) across four star forming regions. We find the spectra to be best fit by two-temperature models that include both standard stellar photospheres and spots with spot filling factors ranging between 0.2 and 0.9 with spot temperatures 1000 K cooler than the photosphere in the median. Such results have significant impacts on measurements of effective temperatures, which in turn alter the masses, ages, and inferred mass accretion rates. For a sub-sample of fifty stars with magnetic field and surface gravity measurements from high resolution spectroscopy, we look for a correlation between starspot filling factors and stellar magnetic field, finding no such correlation. These results highlight the importance of starspots as a measure of stellar magnetic activity.