Sounds like there was too much air in the mix. When you put down the mix, did you trowel it immediatley or did you "work it in" place? If your going over it w/ a membrane and another mortar bed, I guess filling in the weak spots should be OK.
For proper tiling procedures you can go to
www.tileusa.com This is the Tile Council of America web site. They'll send you a free ceramic tile installation guide.