Consider the following document:

a: &a
  x: 1
b: &b
  ref: *a
c:
  ref: *b

Tree:resolve() will result in:

a:
  x: 1
b:
  ref:
    x: 1
c:
  ref:
    ref: &a
      x: 1

Which is correct safe for the unintended remaining '&a' reference. This happens whenever referenced nodes contains further references. As the reference instantiation process creates copies of the entire referenced sub-tree, including any references, there are now references that are not part of the list of anchors and references created at the start of resolve() and which is used to remove them at the end of resolve() - leaving out the 'newly created' references.

Workaround: call resolve() again (this will collect the additional 'newly created' references and delete them).