Picture shows the problem, additional black windows show up when running Factorio.
[0.15.9] (Mac) Extra windows when running Factorio
Re: [0.15.9] (Mac) Extra windows when running Factorio
This is a known issue, a workaround for this is using the system fullscreen option (green button in top left corner) instead of ingame fullscreen. I hope this gets solved in Allegro, because I don't know how to solve it.