I tried to follow the new Blender 2.8 tutorial from Blender Guru. https://www.youtube.com/watch?v=6OTX3ZdYvEA
It's mentioned at around 8:40 in the video, but only very briefly (and doesn't mention the holes specifically) https://youtu.be/6OTX3ZdYvEA?t=517
Unhide the rest of the mesh before applying the subdivision modifier, as mentioned above. Otherwise, the subdivision won't be applied everywhere/evenly I'm guessing?
I had the same problem and found the answer here, but thought it'd be good to point out that the step is in the tut, but is only very briefly mentioned and easily missed.