Here, in the U.S., such a mystery would lead to the dicovery of voles[i in the garden. Smaller than a mouse (sometimes called [i]meadow mice] ) but with a long nose, they don't like to come above the ground from their burrows. Sticking their nose (and mouth) above the surface, they eat low parts of plants and retreat, leaving a hole about the size of the end of your thmb. Set out a small mouse trap or two baited with peanut butter overnight and see what you catch...
Alternatively, dig into the little hole you see and, if it is voles, you'll find a very small tunnel that they use for a runway just under the ground.
Finally, I just trap the little suckers, but if you're uncomfortable with killing them, try a drop or two of peppermint oil down each hole you find. They hate the stuff and soon leave the area. You might have to re-treat the area if it rains...
That's my story and I'm sticking to it!