Nets can be connected or combined in a couple of ways. One is to give all wires the same net name by manually typing in the net name when the wire(s) are selected, and the other is when wires are connected to port with the same Value text. It looks like many of your Ports have a value of “Port_Input_Pin”. The reason for this is: when you copy and past a component, the net (or future net connection) will maintain from the component you copied. This is a great feature with sources such as power and ground, but IO pins it can cause issues if the value of the port isn’t changed prior to connecting the wire.
One option to fix this is the following:
- Click twice on the wire you want on a new net
- Delete the wire
- Rename the value of the port or component you are connecting the wire to
- Re-draw the wire connection.