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4yo post, but facing the same issue.

Sorry, I am not able to understand why - or even if it's correct - for the FLANN KNN matcher to retrieve "lonely points"

A workaround could be to filter the matching "lonely point" :

( found at )

good = []
for i, m_n in enumerate(matches):
  if len(m_n) != 2:
  (m,n) = m_n
  if m.distance < 0.7 * n.distance:

NB : in your snippet you don't use the indices, so you don't need to enumerate matches