Bad loop, I don't think it should work like this.

The hydrogen twisted around to the filter via its orange "output" and started running back to the vent blocking the gas filter from working and clogging up all the works behind it.

the ghost pipe section is what I removed to "fix" this problem, what I was hoping for was to feed out of the gas filter and into that line.  Alternate fix would be to put a gas bridge heading from filter to that junction but really?

Not sure what your problem with this is. You gave it an exit and it's gonna flow to it half the time. The filtered output only adds to the pipe under it, just like the bridge is doing, and it is also gonna flow up half the time and down half the time.

This is a bad design anyways as the hydrogen is trying to reach the vent, while the filtered output is trying to go downward.
This conflicting flow is gonna cause dancing packets as each source is trying to reach its own destination.
 

but it didn't, the hydrogen coming from the pump above looped through the orange to the white to block the gas filter

  Most things don't pump from green through green to white, but this went green(Gas bridge) to orange(gas filter) to white(inlet of compressor that gas first came from.  It created a closed loop clogging the filter and just cycling hydrogen back into its own room