A bit hard for me to explain, but I usually pre-pipe my refineries so I can convert them to advanced processing later. In 0.16 this was no problem. In 0.17.9, the refinery has output crude in to the pipes that were to carry water.
The workaround would be to pump water into those pipes before setting the recipe and connecting crude, but you can't do this either since the both inputs want crude and that is what the pipe is set for.
https://imgur.com/Q62P2KO
[0.17.9] Refinery outputs crude to the other input connection
Re: [0.17.9] Refinery outputs crude to the other input connection
That is not an output, the input simply defines what a connected pipe can take in.