Factorio Forums

When having an underground pipe connection, then placing a ghost image of another pipe that would connect to the existing one, the existing pipe automatically connects to the ghost image rater than it's real counterpart. ( leading to a functional pipe connection to stop functioning, as the game thinks that the real end is connected to the ghost end )
Will upload screenshots / videos later.

I believe this is a known issue, partially stemming from the fact the game can't determine if the real end (connected to the ghost) is supposed to be connected to the ghost or not (e.g. built from a blueprint, and a robot put down the real end first).

Yes, this is intentional. A ghost is usually the intended connection so it does not allow connections over it.