Hi,
The confidence interval is based on estimation of the error for the whole model. The error can be estimated as long as you have degrees of freedom that are not required for model parameter estimation. Basically, as long as you have more rows of data than parameters in the model, JMP should be able to estimate error and confidence intervals.
This is not an independent estimation of error for each unique combination of conditions based on repeated measures for each treatment. That is not how multiple linear regression models work.
For a proper understanding of confidence intervals and how to interpret them I would recommend you get into the mindset of statistical thinking. And there is a really good free online course for that!
I hope that helps,
Phil