The trick to filleting just one side of the hole is to carefully select the one edge of the hole to be rounded off. If the face of the hole is selected, both ends will be filleted.

What are the dimensions of the shaft, hole and fillet?

Here's a Tip: When selecting geometry, hold the cursor over the feature for a few seconds before pressing the mouse button. The feature will highlight (turn orange) and the cursor will often change to show a small graphic symbol (such as a curve, or a line) to indicate what the cursor sees.