This issue is related to issue
#221. When the user has a node with exactly two parents, goes to the tab "Node properties - Parents" and tries to delete the two parents by starting to the delete the last parent (appearing below), after that the button "Delete" appears disabled and there is no way to enable it to remove the other parent.
This situation can be easily generalized to any node with more than two parents. The behavior can be reproduced by seeing that after the last node is deleted, the button "Delete" is disabled even after the user clicks on the "new last node".