I just had the crank shaft seal replaced in my Encore after taking it the dealer for a squeal type noise whenever the air con came on. the noise has gone now but is this unusual to have replaced the crank shaft seal already being almost two years old.

The dealer should have that information, all we can only offer is a guess since we didn't have the vehicle present for inspection or testing... Now, based on your information .. I suppose it's possible that oil had leaked out of the front crank seal onto the drive belt .. then when the "air came on" it caused the "squeal type noise" from belt slippage due to the belt being under the extra load, of the A/C compressor turning on.

Yes it sounds unusual unless they are having a problem on that particular engine or some line,string,ect got wound up in it. Did they cover it under warranty?