I see J1, J2, J5 and J6. That is 4 footprint and they must have (at least) 4 separate schematic symbols. KiCad does support splitting a single footprint into multiple schematic symbols (For example a TL074, where each of the opamps is shown separately in the schematic) but not the other way around.
I also do see ratsnest lines, so KiCad does recognize connections. But overall, I do not understand what your problem is. It is easier if you:
- Make a copy of your project. (Save as… with a different name)
- Delete most of the other circuitry, (It’s not relevant here).
- Delete the fp-info-cache file (it’s big, but not important) and the backup directory (not interesting either)
- Zip up the project and post it here.
However, as an automated anti-spam measure, new users can not upload files. See the link below for more info.
Alternatively, also post a picture of your schematic. How many connector symbols are there on the schematic? and how do they relate to these footprints?