I had to google "grove connector in order to understand what part you were referring to. Connector46/47 were based on grove connector provided by Old_Grey 
Basically Fritzing doesn’t place the drawning wires at the connector middle point (x,y) but instead to one of the corner (Bottom left). I had no idea about it 
What? I was looking for such feature as search bar but never found it.
New tip of the day 
You mean connect them together using internal connection, so they get highlighted if something is connected like “GND pin 1” and “GND pin 2” as example?.
What I should do? Move the yellow header to fit 0.1" grid or let it be?
But if I fix the breadboard alignment, I should fix the pin alignment too 