I have a simple theory to explain both this and "dark matter".
Dark matter, and this "hole" are areas of space that exert gravitic fields (in other words we can tell that something is "there"), but we can't see the the stars themselves.
Dyson Spheres would do this.
It is possible that an alien race, if one exists, would expand by creating Dyson Spheres around every star they could reach.
A Dyson Sphere, for anyone that doesn't know, is a massive, thin metallic sphere surrounding a star that captures 100% of its sunlight and converts it to useable energy. A single Dyson Sphere around our own sun would give humanity trillions of times more energy than we currently have.
Dyson Spheres would give an alien race 100% of the available energy in the universe they controlled and would give them the enough energy to expand throughout the universe at close to the speed, or possibly faster.
It would also make any distant areas of the universe appear *to us* as though they have vanished (they would emit no light yet still show measurable gravitic influence on everything else in the universe.)
Believing in alternate universes is effectively the same as saying "anything can and will happen". It might be true, but it isn't very scientific. It's no more likely than saying "God is a pair of tennis shoes and the universe is ruled by the colour purple, except on red days."
As far fetched as it sounds, an alien life form colonising the universe with Dyson Spheres is a simpler and more logical explanation for "missing" parts of our galaxy than entire alternate universes. After all, the purpose of all living things (on our planet at least) is simply to replicate and spread.
Theoretically we could do this now using solar tech without breaking *any* laws of physics. There's no reason a civilisation more advanced than us couldn't have been doing it for billions of years.