Yes, depending on the MSFS Traffic settings, MSFS could be generating online/offline traffic in addition to the traffic generated by the FS Traffic module.
To ensure that FS Traffic is the only source of traffic generation in the simulator, we would recommend double-checking that the MSFS Traffic settings match those in the Quick Start Guide on pages 8 and 9 of the FS Traffic manual: https://downloads.justflight.com/products/JFF003616/FSTraffic_MSFS_manual.pdf
Mark - Just Flight