"Water was dripping through a hole" is correct.
"Water was dripping from a hole" is correct, but it implies a point of view. It suggests that the hole is above you--in a roof, perhaps--and that you are watching the drip from below.
"Water was dripping across a hole" is wrong. In English, we do not use "across" for motion that is inside something. We see "through" a window, not "across" a window. We run water "though" a hose, not "across" a hose.
If there is a hole in a road, but it is not deep, you might "drive across it," but that is horizontal motion. Water cannot move that way. It can't flow or drip "across" a hole.