Computational simulations have become a critical part of computational science, which is being described as the third leg in this century’s methodologies of science. Computational simulations have also become a critical element of learning experiences as they can provide engineering students with the ability to do things that they could not do in the real world. This study explores engineering graduate students’ perceptions related to aspects associated to the transparency of the simulation tools. The results of this study show that most of the students interviewed found using computational simulations as useful for their learning. However, a transparency paradox was identified. A proposed solution to the transparency paradox may be the implementation of scaffolds together with three different levels of transparency.