IIRC the e03 six-cyl 66L tank has two versions. The early one (<87?) has two pumps. The later one has a fuel siphon. Fuel passing through the siphon from the passenger side pump pulls fuel out of the driver's side of the tank as it flows through. You're sure the lines are right? If not, you could be pumping gas into the vapor recovery system...but if you have an e36 I have no idea.
That filter canister should only see gasoline vapor, of course. When fuel gets warm it expands. If the fuel system was totally sealed, something could rupture. So there's an expansion tank for that in the rear fender. That's connected to the filter canister. The filter can gets vac from the motor so those fuel vapors can be safely burned. The filter canister allows air to enter & leave the system but filters the gas vapors out with activated charcoal. I'm pretty sure there is a one-way valve on the engine side of the filter...check to make sure it's facing the right way. The arrow molded into the valve housing should point toward the line that goes to the motor.