By definition, metacognitive processes may monitor or regulate various stages of first-order processing. By combining causal analysis with hypotheses expressed by other authors we derive the theoretical and methodological consequences of this special relation between metacognition and the underlying processes. In particular, we prove that because multiple processing stages may be monitored or regulated and because metacognition may form latent feedback loops, 1) without strong additional causal assumptions, typical measures of metacognitive monitoring or regulation are confounded; 2) without strong additional (...) causal assumptions, typical methods of controlling for first-order task performance (i.e., calibration, staircase, including first-order task performance in a regression analysis, or analyzing correct and incorrect trials separately) not only do not deconfound measures of metacognition but may even introduce bias; 3) that the first two problems cannot be solved by using simple models of decision-making derived from Signal Detection Theory. We conclude the paper by advocating robust methods of discovering properties of latent mechanisms. (shrink)