I had a very similar situation just a few days ago! The regenerating of the global objects on the global layers.
And, as far as I found, the global layers seems persistent on every layout, by destroying every objects on a layout's end, and then regenerating them on the new layout. But here, the objects are also global objects, they are not destroyed on the layout's end, so they remain, and the new layout's new objects (for global layer) are generated (without checking whether there is remaining objects or not.)
I don't know why it should work this way, but anyway it does...... maybe we should ask Ashley. I was making a HUD too, faced this problem, and solved the HUD's duplicating issue by this way: https://www.scirra.com/forum/how-do-i-prevent-global-objects-regenerated_t166734 take a look at the reply starts with 'I solved the problem!'