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We review the ambiguities in the nuclear information extracted from breakup reactions, focusing on those originating from the description of the reaction mechanism and the overall ambiguity inherent to their interpretation in terms of shell occupancies. We present the current discussion about nucleon knockout reactions and how the understanding of the reaction mechanism would help reducing uncertainties. For the former, we consider the case of ¹¹Li, due to the existing large data set. For the latter, we recall the paradigmatic example of the electro-dissociation of the deuteron to address the question of the scale and scheme dependence from the theoretical framework used for the interpretation.