If that is how it is connected (and works) in real life then that’s also correct in Fritzing. The red dots only indicate no connection, since they aren’t being used that is fine here and isn’t your problem.
This looks to be caused by wires added (or incorrectly connected) in schematic and/or pcb. I’d suggest that you first move the parts in pcb (noting that many of you resistors are currently SMD which you may not want) so no pins overlap which makes routing (and not creating unintended connections) easier. You should do all the connections in one view (likely breadboard in this case) and once that is complete then follow the rats nest lines in schematic and pcb to make the routes the same. If you connect a wire incorrectly in schematic or pcb views that will reflect back in to breadboard view and break it. Sometimes (which may be the case here) this corrupts the sketch and you need to start again.
As noted above I’d suggest deleting all nets in schematic and pcb then work on breadboard til it is all routed and correct before moving on to schematic and pcb. In breadboard the wiring for the grey leds at the top looks to be incorrect. The data wire from the Arduino needs to go to din (not dout as it is now) on the other end of the module. As well you have a short from +5V to ground somewhere (probably in one of the other views) because if you click on a ground pin all the +5V pins also light yellow indicating they are connected together although breadboard looks correct to me. I think you may have a corrupted sketch (and thus need to start again). There are traces and vias in pcb view (which are likely wrong) but even when I removed all I could find it still says there are two nets routed (which there shouldn’t be).
Peter