Although ecological systems at varying scales involve non‐linear interactions, learners insist thinking in a linear fashion when they deal with ecological phenomena. The overall objective of the present contribution was to propose a hypothetical learning progression for developing non‐linear reasoning in prey–predator systems and to provide empirical evidence for one part of this progression. Pre‐service teachers followed three teaching units that involved a game simulation of the prey–predator system. Participants predicted how wolf and deer populations would evolve in a hypothetical forest, and then they used the simulation to generate data, construct a graph, describe their graph, and compare their predictions with graph description. A new learning context was introduced and new predictions were requested to investigate whether participants would transfer former learning experiences in the new setting. Analysis of learning products revealed the “messy” character of learners' intermediate steps. Some participants succeeded in identifying aspects of metamodeling knowledge, but this was not used in their new predictions. Graph description could either perpetuate or challenge linear heuristics depending on the strategy participants followed. There were a number of participants who misrepresented prey and predator population trends as “inversely proportional,” which indicated that there is a possibility of regression to the lower anchor. Linearity and proportionality might have re‐surfaced during the learning activity sequence and linear heuristics could have been so powerful as to distract learners' attention from axes labels. Learning products constructed by learners during learning activities included crucial benchmarks to diagnose learner performance and indicated proper timing for feedback provision. Overall, the implications of the study highlight the importance of using learning products to enact formative assessment. Directions for future research are discussed. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 53: 1447–1470, 2016