They are probably referring to dimensional stacking and how that affects the the overall size and performance of parts. for instance, if I have a part that the dimensions are +/- .002 for each measurement and I measure from a corner to .25 inches and then from that point to the middle of the part at say .75 inches then those to dimensions could be +/- .004 and so on. this is why we try to use datums and dimension from one point on a part to avoid stacking up a lot of tolerances. This process would be the same for an assembly as well. So Stack up Analysis is really just evaluating the tolerances to tell whether or not they are going to adversely affect either your part or assembly.
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