Those are not holes, they are actually mounds. But this is the first time I have planted anything in this bed, so I have no idea how the plants are going to grow here yet. Right now my biggest concern is not the plants sinking deeper, but it will be trying to keep the critters from digging them up! I have at times noticed some plants in different beds seem to be working their way a little deeper(my main concern is my Amaryllis) but I can't tell it has caused a major problem yet with any plants. I assume you must have sandy soil?
Sometimes I plant very shallow and it seems the plants pull themselves down, and sometimes I see plants that seem to be pulling up their roots like they are planning on leaving.