I did the same and got the same annoying result so I did another fix procedure: Dragged a selection box for each pair of path nodes then used the “Merge selected nodes”.
Okay, I will do the last fix to the breadboard view since I didn’t check the schematic neither pcb view because I hope you did them @vanepp.
EDIT: There you go DFRobot-PH-sensor.fzpz (69.4 KB)
Final fixes to the breadboard view: changed the resistor components to the ones from adafruit parts because look better for this board. Also added the trimmer potenciometer and removed the blue border lines.