I am seeing a similar or the same bug in 1.9 pre 4, but only with players. I am not sure if it's the same bug or not (as discussed in the other comments on this issue), but my report was marked as a duplicate. The issue seems to be fixed when the invisible player disconnects and reconnects to the server, but it does seem to happen a lot, especially when travelling to the end.
I am seeing a similar or the same bug in 1.9 pre 4, but only with players. I am not sure if it's the same bug or not (as discussed in the other comments on this issue), but my report was marked as a duplicate. The issue seems to be fixed when the invisible player disconnects and reconnects to the server, but it does seem to happen a lot, especially when travelling to the end.