When modifying pipe ghosts, it seems to like, reset something? Like, if I have a pipe ghost that's connected on all 4 sides, and I block the left side, now it's connected on the remaining 3 sides. Now if I block the right side, instead of being connected on 2 sides (top+bottom), it's connected on 3 sides (top, left, bottom), having entirely forgotten that I blocked it on the left. The same issue does NOT occur on real pipes, only ghosts; so guessing something to do with however you're storing the data on ghost pipes.

This should be fixed in 2.0.9! Since I can't search for fluids through the ghost entity, you can allow fluids to mix by editing a ghost pipe's connections. However I'm going to consider this working as intended, as I can't think of a good fix. Also some monsters (complimentary) like to multi-purpose a single pipeline for multiple fluids, so I wouldn't want to make things more complicated for them.