Darker areas on paint where I previously applied filler
I would wait for a couple of days to see if the filler (which maybe absorbed water from the paint) dries completely and then the color matches.  But since you didn't prime the filler (or maybe it didn't dry completely), possibly where it was thick, it has modified the color of the paint.  If the area is still darker after a couple of days of letting the paint/filler dry, then I would apply primer to those areas and repaint.  Hopefully you can use the same roller nap and get a good match on texture so you will not have to repaint the entire wall.