I have to say that 2/3 confusion is the most common mistake that I (and others with me) make.
If I don't get a reply on 12X.XXX, I'll quickly try 13X.XXX, or vice-versa, before going back to the original frequency. It doesn't seem to matter how carefully you listen or read it back, you often end up on the wrong channel.
It seems much rarer to make that kind of error when accepting altitude clearances, although RVSM might be increasing the chance of this happening. Virtually everything on ATIS is susceptible to mis-interpretation but at least you might have a forecast/old actual to pick up any gross errors from.
I notice that more and more airfields require you to read back the QNH as well as the ATIS letter - a possible 10hPa difference in setting could be embarrassing, at the least...
One last observation. I don't have a problem in normal conversation on the ground/in the flight deck in telling the difference between "two" and "three", let alone "TOO" and "TREE". Maybe the bandwith limitation on VHF R/T reduces the difference between the two spoken words...?