And for your extra circles. I tend to agree with 3Dogs here. I do see 4 circles (cross eyed?) The yellow one is probably a pin one indicator on Silkscreen, and the grey circle a pin one indicator on the Fab layer. But what is more important here is to learn to check such things for your self. So load your footprint into the footprint editor, and then examine the properties of all it’s constituents.
If you look at the datasheet for JST PH series connectors (here) you will see that the top entry connector is labelled -BnB- and the side entry is -SnB- where n is the number of pins
In my experience JST are better than most manufacturers in terms of consistent product labelling but you should always look at the datasheet to confirm