Residuals from linear regression show only the mean residual, not each individual replicate.

 This is indeed a limitation in Prism's linear regression analysis. Even if you enter replicate values in side-by-side subcolumns, Prism only tabulates and plots the mean residuals, not the individual replicate residuals. 

Easy to work around: Instead of using Linear regression, choose Nonlinear regression. Then choose the straight line equation to fit to. Not only will you get individual replicate residuals, but you also can use outlier elimination, differential weighting, and more diagnostic choices.