Why little holes/dots when I apply joint compound?
There have got to be many ways to minimize the bubbles.  These kind of problems you deal with when finishing drywall require a certain amount of skill that, for me, comes only with experience.  That said, I have a few ideas:


Add a little bit of water.  The further along in the finishing process, the thinner the compound should be.
Mix well, even if you add no water.
"Work" your mud with a knife in your pan (or on your hawk) for a few seconds.  
It's hard to tell from the pictures, but it looks like your application could use fine tuning.  a. Apply the mud to the wall as you have done.  b. Remove mud from the knife and, putting pressure on the left side of the knife, go back over application. c. Do the same for the right side. d. With light pressure in the center, go over again.  This will help to better feather out our edges.