When I try to bevel the edges of the holes, it ends up going into the hole instead of beveling outwards.
Not sure why it is doing this, please tell me if I’m doing something wrong.
You probably forgot to apply scaling in object mode.
Exit edit mode. Select ball. Press Ctrl+a and select “rotation and scale”.
I tried doing this to test it, both before, and after moving, rotating, scaling. Not applying. None, nor the cumulative effect, seemed to produce this effect. I also tried flipping some normals but that did cause distortion but not this effect shown in the OP. All panel setting are default.
I know it has happend in the past to me for unknown reasons, and possibly Applying R, S, can sort it out. However it seems not to produce it here.
So I am no help at all!
No idea what makes it happen.
I think you sent us the wrong direction. Because there is a Bevel function. And with that in mind, your outcome is strange.
But I do now realize that you are not beveling, but just creating an EDGE LOOP, using Ctrl r. With you can create a bevel, but not a simple task.
You mesh topology is very good and a simple bevel is a mouse click away.
Select the edge loop of the hole and press Ctrl b to bevel edges.
Move mouse inwards or outwards to select a size. And use scroll wheel to add details.
Check your mesh also on doubles …
NO he has the bevel panel open, so he is beveling.
However, I think you put in the answer at the very end!
I recreated what he shows this time, by creating the loop via ‘bevel vertex’. Hitting extrude, clicking without moving or esc would do it too. Then extruding properly into the ball. This created the doubles! Then selecting the verts in the loop, so long as you get the ones attached to the inward extrusion, not their doubles that did not extrude. Then beveling that selection creates inward only ‘bevel’ or as it looks like, just the one loop cut inside the hole!
So solved 
The reason it is happening is you have double verts on that loop you want to bevel.
A select all in vert selection and ‘Merge by distance’, should remove those doubles.
It is, if I am right, a common, and Mikey warned, problem of extrude. You imagine escaping out of the action means nothing has been done, but it has made the new set of verts ready to be moved in the next part of extruding. Of course, as they are exactly in the same starting place as the loop you wanted to extrude they are invisible to the eye and you think you have canceled the operation, so why expect them to be there.
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Thanks that fixed it.
Clever deduction !
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