My extremely rough and most likely wrong guess is that you had a smaller stack enter from Khandesh to Marathwada, and a bigger stack enter from Desh or Bijapur. I'm guessing the bigger stack can siege either Marathwada or the capital fort if their return province is Pune, or if the capital does not have an extra fort then you could walk straight through and have their return province be the capital. If you then combine both stacks at Marathwada it would reset the return province to the capital. Or something along those lines.
That or the Marathwada fort was mothballed so you could walk straight through.
Is your tooltip covering another fort?
Tooltip isn't covering another fort.
You managed to list two of the other ways the illegal move is possible (unit shuffling from origin point, immediate move to take advantage of mothball). The latter is important; any move order issued that is valid will stay valid even after the fort is created. That opens up additional possibilities:
1. Fort was constructed after the move order (not likely, but possible)
2. Troops with no movement restrictions at present (exile) ordered past for then clear exile, orders still valid.
In addition to the one I missed above, the possibility that I straight up got military access in Vijay and just landed there, and yours we're now over 4 different ways to allow for an otherwise illegal-appearing move.
bbqftw did something similar to this in another thread...and none of those arguing in favor of the fort system could answer his questions either. The more one actually understands the rules, the more obvious how broken they are. And yes, that means there are conditions where AI can ignore your fort ZoC, because there are conditions the player can do this also...