I can confirm the issue: also I see nodes on the waterway which are NOT part of the way. I find them on many waterways in Laos. I checked one of those nodes http://www.openstreetmap.org/node/1550235958 and found out that the changeset was created many years ago in an old version of JOSM - by the same user as your example.

Actually, such nodes should be easily found:

  • download the data in JOSM
  • select all
  • run the validator
    These nodes should show up under validation warnings.