Bad filter technique

I'm using a filter for the first time. Setup is the source keg is hooked up at 2 psi and piped through a filter to the spear-side of another keg. The beer was cold from being in the fridge overnight and had not yet been carbonated. Everything was fine until I left the garage for longer than I thought I would.

When I returned it had finished pumping the beer from one keg to another and was slowly pushing CO2 though the filter and bubbling up through the keg, producing a nice layer of bubbles on the top.

I've read that it's bad to aerate the beer as it produces staling reactions, but I did it with CO2 instead of air. I tasted it afterwards and it definitely had changed the flavor for the worse. My question is, is the flavor change temporary and I've just given it a head start on the carbonating process, or did I just "stale" the beer?

CO2 is tasteless, and more importantly will not oxidize your beer (of course). If you noticed a change in taste it was due to something else in your process. In the future, instead of using a filter try gelatin finings. They are easy use, and will result in crystal clear beer in 1-2 days. IMHO, it's a lot easier at the homebrew level than mechanical filtering.

Part of the reason I'm wondering if something happened was that I did two batches back to back, the only difference being that I watched the second one and made sure it didn't foam up. The second one still tastes fine. I had "primed" the filter with water, then dumped the early mixture of beer and water to avoid watering down the beer.

You want to flood the filter and destination keg with CO2 before doing anything then there is no oxygen to worry about.