Versions:

• Mod: 1.1.6
• MC: 1.20.1
• Forge: 47.3.12

Breaking and placing the controller causes the pipes to disconnect from the Turbine Port (visually they appear connected but logically they are not). In the video, I show a few more cases https://www.youtube.com/watch?v=jsFRIAyYB1Y. I'm not sure if it's related, but I had a similar problem with single block machines (e.g., centrifuge). After restarting the server, Refined Storage could not insert liquids. Replacing the crafter helped.