I'm experiencing this bug as well. Putting the logs into a chest and going back out resolves it but the moment I get logs in my inventory again it does it again. Saving and leaving world did not resolve it, nor did a full restart of the client.
Video of it happening here (youtube link)
edit: this is also happening with picks, shovels, and pretty much anything where what you break is what you pick up. Stones that turn into rocks don't trigger this, nor do meteoric iron nodes.