where is the small wet area in relation to the drain or walls? Never heard of that, but I'll take a few guesses:
This is obvious, but check to see if there are any small cracks in the tile or grout around the wet spot where water might be getting behind them
If the spot is near the drain, I'd assume that not all of the water is being drained down the drain pipe, but is instead getting into the area surrounding the drain pipe, enough that even after drying off the wet area, there is enough water sitting underneath the mortar or tiles that it will wet through again to the surface.
If the spot is near a wall or the corner, I'd assume that water was getting in from behind the wall somehow and creating the same problem as above.
One final though, and I doubt this is it, but maybe your mortar bed didn't dry thoroughly and that one spot stayed wet? But I highly doubt that would have enough moisture to get the top layer of tile wet.
Maybe search the web for a tile only forum. The Journal of Light Construction has an online forum, supposed to be just for pros, but I'm guessing only pros will have a decent answer to your problem. There is a dedicated tile forum within their forums. It is www.jlconline.com