The test area selection is done based on a single layer in the Arizona Xpert Engine. Once the test areas are selected, corresponding test areas are cropped at exactly the same locations from all the other layers. When you have different sizes, scaling or offsets for any of the inputs the content of the different print layers may not match when sampling. Likewise, the content may not match if you have multipage documents with different page sizes.
When using merged layers, prefer using the merged layer as input for the test area selection. Using the individual inputs when selecting the test area may lead to unexpected results.