PCB routing mismatches the schematic
It is all about the name of the nets (the interconnections between the parts)

As you draw it, it is very clear that there are two distinct voltage sources with their positive terminal not being connected together.

But from the logic of most circuit design programs, each piece of interconnection line has a name, and all lines with the same name are electrically connected together. This allows to omit interconnections, if they make the schematic less readable.

For your desired behavior, the interconnections from the two sources need distinct names.
Often, pins of sources give names to attaches interconnections automatically, and I guess, that's what happened here.

One often needs two identical voltages, one for analog, and one for digital parts of the circuit. For convenience, the part libraries often have two similar parts for this.

(this answer is quite universal, and applies to other design tools like EAGLE, too)