This happens when a playlist is being viewed, and the search box has been used to narrow down to a few tracks in the playlist. Right-clicking one of these tracks and selecting "Remove from playlist" will refresh the playlist and a track will be removed, but it won't be the track that was right-clicked. It looks like it's taking the number of the track within the search results and then removing that number from the playlist as a whole. For example - removing the second search result will actually remove the second track in the overall playlist.