You get on a 3 degree slope, say, down to the threshold. When you look at the runway, however, it looks more like you're on a steeper slope down to the runway as you say. Thus you conclude that you are too high and descend at a greater rate to intercept what you believe to be the true 3 degree slope. You have therefore dropped below the desired slope, and your usual approach 'setup' will cause you to land short.

To visualise, draw two parallel lines at 3deg to the horizontal. On the end of one draw a horizontal 'runway', and on the other draw an upsloping 'runway'. Note that the upsloping runway is at a greater angle to the approach than the flat one, despite it still being a 3degree approach.