Septoria is normally an outdoor cultivation problem, but anything could be possible. Look for the spots to be greyish-white to brown to start with.
I'm still leaning to a def. but pH is key.
Can you test the pH first though? I would definitely look at that as it can lock out nutrients and cause all sorts of problems.
Let me know please.
Sorry I haven't grown an Auto yet so I can't say how filled out they should be, hopefully someone else can pop in on that.