Sky Rogue is made in Unity 3D, which can occasionally run into a quirk with the resolution. Here's a fix that I've used on other games that either get that error or run into a blank screen.
Go to ~/.config/unity3d/Fractal Phase/Sky Rogue/ and then edit the prefs file. The first few lines will be the Screen Manager settings. Edit them to look like this:
<pref name="Screenmanager Fullscreen mode" type="int">1</pref>
<pref name="Screenmanager Resolution Height" type="int">1080</pref>
<pref name="Screenmanager Resolution Use Native" type="int">1</pref>
<pref name="Screenmanager Resolution Width" type="int">1920</pref>