It doesn’t remove anything - it just snaps nodes or objects to other nodes or objects.
What do you mean by “it snaps them together but they don’t overlap”?
This might be bit of confusion with how it works. When you start dragging something, the start point also has to be a snap point if you want that placed perfectly with something else.
For example, if you have a square, when you’re in selection mode, you’ll see the cursor change to one of the snap indicators when you’re over a node, the center of a line, or the center of an object. When you can see that cursor change, if you grab the object then, the starting point has also snapped.
If you don’t do that, you could be snapping just a grid point or arbitrary point along a line to the destination snap, which isn’t what you likely want.