This is usually caused by bad sequencing within one or more parts, particularly when doing chain-crops with a crop overlap.
Example:
•Do an array of chain-crops with a +ve chain cut overlap set.
•Reorder one of the parts internally, so that the left hand crop is cut BEFORE the right hand wiggly cut around the parts (bad! This will not cut properly):
•Plan Grippers, this warning is likely to appear:
'While planning grippers, unable to compute skeleton separation, possibly bad internal part sequence