I started seeing same warnings but they weren't there before.
Not sure if some behaviour on macOS changed or is just noise, but to on the safe side I changed my implementation to open the first window on my app.
The key is to use orderFrontRegardless() instead of makeKeyAndOrderFront(nil)
Example
func applicationDidFinishLaunching(_: Notification) {
let window = Window()
window.makeKey()
window.orderFrontRegardless()
}