I always have water in my portafilter after extraction. Not like a pool of standing water, but that the puck is like a bog, full of water but you could walk on it. I usually leave it in the machine for a bit, usually while I enjoy my drink, waiting for it to cool down before cleaning.
It is not a big deal. Some machines do that.
Below is a link with a short article that addresses the issue...but I wouldn't fuss over it. Some machines just produce a soupy puck.
http://www.wholelattelove.com/articles/troubleshooting_espresso_routine.cfm