By default radially attached parts aren't passable. In the VAB in the CLS menu there is an "Enable Optional Passable Parts" option. You have to select CLS: Attachable Surface on the station part. or CLS: Surface attachable on the docking port. I don't know if you need both selected for it to work. The parts from SSPX have these selected by default, but only if "Enable Optional Passable Parts" is enabled. Stock science lab or hitchhiker don't have these selected by default. If you are using Ship Manifest there are options for crew transfers to ignore CLS, but the living spaces will still be disconnected for calculating Hab space with life support mods.