An orphaned node is a node that is not referenced by any parent. Any node in Nordcraft has an array of children. That way we can build and render the node tree (html). If a node exists but is not referenced by any other node it is orphaned (root node excluded as that is a special case). Orphaned nodes will not get rendered as they are not included when we build the node tree. Thus they can be safely removed.
How orphaned nodes can happen can be more tricky. It is due to bugs obviously but it could be anywhere in creation, deletion, pasting or something else.