https://github.com/BabylonJS/Babylon.js/issues/2624
This is still an issue for me. Was unable to reproduce on playground, however adding some additional information, maybe someone will have a clue as to what's going on because as of now I can't really use the highlight layer.
When the scene is first loading up (and my meshes are being created for the first time), and a highlight layer is created while this is happening, I see a ton of undefined meshes stored in the highlight layer, which I have no idea where they are coming from. 85 to be exact. (note that at no point am I manually adding any meshes to the highlight layer) - The draw calls are now going from 110 to 220, so there are 110ish additional draw calls being added, even though the highlight layer isn't doing anything.
These mesh ids, also don't appear to be valid anymore.