When you are pouring, pour the stem first. Use a toothpick or something similar to move the stem around and get out any bubbles. Then place the 2 halves of the mold together keeping the stem on the bottom, pour at an angle then stand up to cure. Since I have started doing this I have not had a single stem fail to turn out. Are you using any mold release? I have been using the same mold for about 30 caps now and have not had any issues but I am using castin' craft mold release/conditioner.
Here is one I just pulled from the mold after doing the above and it came out perfect. I poured the blue first, let it sit for 12 hours then poured the white. What are you using to color your resin? I saw what you posted above but what brand is that?