I can see the Partisans fighting alongside the Rebel Alliance but I can't see them attacking a Rebel convoy alongside Black Sun.
And yet...
Mon Mothma was bringing Jyn into their circle specifically because Saw's group would shoot any other Rebels on-sight. So...yeah, "attacking a Rebel convoy alongside Black Sun" sounds about right - that is, if they ever felt like leaving the Jedi template on Jedha. Which they didn't feel like.
Also: Saw had a fear that Mon Mothma had sent Jyn to assassinate him.
I mean, seriously, how much more obvious could it be that they are not on the same side?
When the Rebels say flat-out, and clearly, in dialog that the partisans shoot at them. And are not part of the Rebellion. And Saw is afraid of the Rebellion attacking his forces.
Seriously - these guys are not on the same side.

