This is something I think I have seen in the last few version. Doesn't happen too often, but can be very annoying. On the image you can see in the top right corner pads from a component on the bottom layer appearing below the top (correct) and at the bottom you can see two components from bottom appearing above the tracks on top. The problem appears to be limited to pads only - tracks are layered properly. Browser is Chrome 68 on windows. Refreshing the page doesn't help.  Cheers