It is important when you apply the clear coat (or in the case of a tri coat, the second base color, also called a mid coat, and labeled with a "/2"), to do it very carefully, as the recently applied base coat can be removed by the solvents in the clear coat or mid coat. You need to float the clear coat/mid coat carefully over the base coat, because the second layer of paint or clear coat acts like a solvent and too much pressure applied will remove the base coat. Also, make sure to let the base coat dry a little longer to help with this issue.

It's a good idea to practice your technique for applying clear coat on the test card. Paint a few squares of primer+base coat on the test card to practice your clear coat technique. 

In cases where your brushed repair is large, it can be difficult to apply the clear coat or mid coat without having it remove the base color. In these cases you may choose to spray the clear coat or mid coat from an aerosol, which eliminates the physical application problem because the clear coat is aerosolized and lays down on the base color without the pressure and contact of a brush.