It’s the tool itself trying to save the files.
Just to be sure, I created a new scene from scratch, brought in a mesh, made sure there were no unknown nodes and saved it as both a .ma and .mb file type and attempted to go through the ART process. Same errors as before with the:
Error: RuntimeError: file D:/UE4 Rigging Tools/MayaTools/General/Scripts\ART_skeletonBuilder_UI.py line 8714: Problems occurred with dependency graph setup.
With all of the follow-up errors I posted before.