<Hansolo>That's not how liquid flow works.</Hansolo>

It works if I deconstruct the pipe to the right of the junction, but I kind of wanted that pipe there.

Disconnecting the liquid pump leading into the junction also fixed it. This shouldn't have made a difference as the pipe wasn't pumping anything.

It works fine if I have another output, say from a carbon skimmer connected to it.

Kill these pipes if you want water down there. I'd recommend considering flow direction when planning next base.

 

I think the problem is due to the Algae Distiller fighting with the Sink/other things. They both want to output and flow towards the exit that is under the Natural Gas Generator. I've tried to show the conflicting paths below. If you deconstruct the pipe next to the Algae Distiller everything flows properly.

The pipes have their own special rules for flowing and don't obey what you would see in the real world so you'll have to experiment to see what works.

When looking for problems I try to trace from green to white and see whether there are two overlapping paths that want the liquid to flow in opposite directions.

The problem I see is that you are putting outlets in the path that wont flow past that point without filling it first.  Its not like the real world, if you branch off of the pipe for each outlet then the system will always pump to outlets, insert valves to reduce amount of pumping per outlets connected and you will see a drastic difference.  TLDR inline systems act wanky, branch in and out, green to white

 

It's not a bug. Pumping mechanic is not based on pressure so it don't work like IRL.

Bouncing packets of liquid/gas in pipe is caused by mistakes in connects between inputs and outputs.

I was able to fix this by using a few strategically placed pipe bridges as check valves, which seemed to better regulate the flow direction. I still consider a bug because it is very counter-intuitive behavior. I don't demand total realism from my games, but I do expect a certain level of verisimilitude. If you tell me something is a pipe with liquid flowing through it, its behavior should in some way resemble that of a pipe with liquid flowing through it. Having to consider all of this flow direction and bouncing packets stuff just adds confusion.