Yeah, I don’t think it’s a bug nor an intended mechanic. What you describe here happens to me more than what I wrote about just above. I think it’s a just what happens. 
Maybe at most we could call it a glitch.
I think it’s similar to that situation we have with trying harvest all other nodes too. So, with spider webs for example sometimes the scythe can’t hit it right and you have to try 10 different angles. Same with mushrooms. And the bit where sometimes your tool can harvest from small stones and sometimes it can’t (without the Couch+Attack technique). It’s just how it is.
Bug? I wouldn’t call it that. Annoying? Yeah, I would call it that.