Hi Alex,
This can be dealt with quite easily.
After you've generated your Dense point cloud, just run the "classify ground points" feature which will divide your dense cloud between ground points and non-ground points.
After this proces is finished, simply set the model view to "Dense cloud classes" and manually check and verify if the classification went well by switching back and forth between class view and dense cloud view (with RGB colors).
Photoscan should by default get it somewhat right, i.e. it should classify piles of sand and the rest of the ground as brown "ground" points and all the other points from vegetation/objects/water/noise as white "never classified" points.
If you're happy about the classification just generate a new DEM of only the ground points. You can set this in the Build DEM parameter window by only selecting Ground for the "Point classes".
Once the DEM has been build, double click on "DEM" in the workspace pane to the left in Photoscan. This will open the DEM in a seperate viewing tab. If all went well you will see a hillshaded elevation model that has no noise from water in it.
If the stockpiles are missing from the DEM you'll need to reclassify the stockpiles either manually or by playing around with the auto classify parameters.