Krokul Flute (http://www.wowhead.com/item=152964/krokul-flute) is not flagged as collected on alts (https://puu.sh/A8MK0/fcbf221050.png) when it has been collected by another character on the same account (https://puu.sh/A8NlA/1cc0afe153.png)

Yes, this is a known issue unfortunately. Due the way Blizzard flags (well lack of flagging) spells in the API I haven't been able to get it to properly mark off as collected unless that specific toon learns the whistle.

I think for the next build I'm going to just disable it again though with new recipe tracking as account wide I might be able to get around it. Will need to talk to Crieve about it and see what we can do.