If you're clear flat is yellowing, you either have a bad batch of paint or you didn't shake it well enough...unfortunately, short of stripping the model, there's not much you can do to fix it. Perhaps you can dry-brush some of the base color onto the areas that show up as yellow, to try and tone it down? What color is the figure itself, can you use the yellowing of the clear coat to your advantage, like dust?
In the future, (no pun intended) try using Future Floor Wax mixed 2:1 with Tamiya X-21 Flat Base. It's safer, smells better (like apples), never yellows, and if you screw it up, you run it under hot water before it sets up and remove the trouble spot. Then you re-spray. It's what I use on everything I build, armor, ships, figures, aircraft.
Jeff Herne
Modelwarships.com