I'm a bit confused. You say you ran a 3^3 factorial (27 treatments), but in the picture you attached, it mentions 3 blocks? What are the blocks? What was the model you used? What do the other diagnostic statistics look like? (e.g., R-Square-R-Square adjusted, RMSE, p-values). I assume you are trying to create a useful model. Does the model work?
Try plotting the residuals some different ways
1. vs. run order
2. Save residuals and look at the distribution.
3. Take a look at the leverage plots.
4. Residuals vs. predictor (that is each x)
5. JMP will also plot studentized residuals
It does look interesting. It looks like the first 3rd is quite what you'd expect. The second third looks strange, are these center points? Then the last third look like it trends. None of these may matter if the order is not meaningful.
"All models are wrong, some are useful" G.E.P. Box