We had a similar circumstance about 2 years ago.  Try as we may to figure out what WE were doing wrong we came up with no solid reason. UNTIL we went and spoke with the nurses assisting during the procedures and lo and behold we found the answer.  

The nurses had no idea how important it was to place the biopsies in formalin at time of removal.  They sometimes sat on a piece of gauze for up to 90 minutes before being placed in the fixative.  As soon as we adjusted their behavior - all was well.