Sour is generally caused by bacteria. You may be a sanitation freak (I am too) but it is possible you picked up an infection. If the beer tastes fine before bottling then it may be something with your bottling bucket or bottles themselves.
I get those air bubles all the time and have never been an issues.
Also, oxidation with cause beer to stale faster, and in extreme cases taste like wet cardboard, but wouldnt contribute sour flavors