I assume you created the decal?
There are a couple things that will cause the decal to not disappear under the CA. If the layer of "fixative" on the decal when you created it is too thick then the decal does not have the flexibility to settle into any texture on the surface you apply it to. Also, even on a perfectly smooth surface, the thicker the decal film (with fixative) the more likely it is to show up under the CA.
Another thing is the gloss on the surface of the decal vs the gloss on the surface of the pen. It has been my experience so far that if the CA is not polished and the decal is glossy it tends to show up more. You can either MM the surface to a gloss before applying the decal or use a flat clear when sealing the decal....kinda depends on the final finish you are trying to achieve.
How long are you waiting between applying the decal and finishing the pen. I always wait at least 24 hours.