As with any Medieval church there were a large number of graves, they would have known there were graves there but avoided disturbing them unnecessarily for a range of reasons. If there was a garden the feet could have gone when something was planted, they would have just have been a few more bones of many found in the area.
I'll buy that.
Expect that if there are more excavations on the site then a jumble of bones and perhaps even bodies that would have been buried in coffins should emerge. If there are very few bones from the site - i.e it was disturbed regularly over the centuries after the monastery was demolished, my "they knew it was there all along" conspiracy theory holds water!