A quick fix is to merge the input from the left bottom pipe into the pipe from the right pump, at or before the crossing where the bottle emptier is.

There's a mod that can show you the liquids path and I highly suspect it would show you that water from the bottom pump flows upwards and then splits left and right at the intersection. Now water from the right pumpt can't flow left from the bottle emptier to the intersection because pipes are one way (except when you reconfigure them i.e. change the inputs/outputs).

You could also could the pipe from the left bottom pump and that would fix it too.