From the very first measurements made by the magnetometers onboard Swarm satellites launched by European Space Agency (ESA) in late 2013, it emerged a discrepancy between scalar and vector measurements. An accurate analysis of this phenomenon brought to build an empirical model of the disturbance, highly correlated with the Sun incidence angle, and to correct vector data accordingly. The empirical model adopted by ESA results in a significant decrease in the amplitude of the disturbance affecting VFM measurements so greatly improving the vector magnetic data quality. This study is focused on the characterization of the difference between magnetic field intensity measured by the absolute scalar magnetometer (ASM) and that reconstructed using the vector field magnetometer (VFM) installed on Swarm constellation. Applying empirical mode decomposition method, we find the intrinsic mode functions (IMFs) associated with ASM-VFM total intensity differences obtained with data both uncorrected and corrected for the disturbance correlated with the Sun incidence angle. Surprisingly, no differences are found in the nature of the IMFs embedded in the analyzed signals, being these IMFs characterized by the same dominant periodicities before and after correction. The effect of correction manifests in the decrease in the energy associated with some IMFs contributing to corrected data. Some IMFs identified by analyzing the ASM-VFM intensity discrepancy are characterized by the same dominant periodicities of those obtained by analyzing the temperature fluctuations of the VFM electronic unit. Thus, the disturbance correlated with the Sun incidence angle could be still present in the corrected magnetic data. Furthermore, the ASM-VFM total intensity difference and the VFM electronic unit temperature display a maximal shared information with a time delay that depends on local time. Taken together, these findings may help to relate the features of the observed VFM-ASM total intensity difference to the physical characteristics of the real disturbance thus contributing to improve the empirical model proposed for the correction of data.