More precisely, when the obsidian pipe tries to suck the arrow into it, as shown in this log http://pastebin.com/11x4QhzP
After restart the arrow is stuck still on the end of the pipe and can be retrieved as normal.

This bug occurs with dispensers and striped pipes, but not with bows, since the pipe doesn't attempt to suck in the arrow in that case. I don't know whether that is intended behaviour.