Most likely:
Your source mesh is an object made of several surfaces not being connected.
If it is a scanning result there may be small outliers (scanning errors) floating in space.
If it is a modelling result it might be just a combination of different, maybe intersecting partial objects. In this case you need to construct a single watertight mesh first (several ways... depends on the very case ... please post a screenshot).
Or:
Your source mesh is a single watertight shell but the cut hits the object several times (e.g. cutting off the peaks of several mountains)
