This is definitely a problem, and it's been reported before and some really helpful people posted detailed workarounds here. I think linear farm designs start out working but fail after a while. I'm not sure what triggers the farm tile to fail and block the water flow.
Near as I can tell the unwritten rules of pipes are:
Be careful how you layout inflow and outflow nodes. You want your pipe flow to be unidirectional. If your pipe doesn't have a clear sense of "direction" water blobs will get confused in your system.
Don't just link up all the outflow nodes and inflow nodes. Make sure there is an individual pipe going to each one.
Use gold amalgam instead of iron ore when you build your pump for pumping boiling hot water.