In most residential building construction, the production system design relies on the assumption of linearity per zone and per story, thus, takt-time schedules and flow lines are produced accordingly. However, in practice, such smoothness is difficult to achieve due to non-linear and non-repetitive projects. This research aims to identify the main challenges of the production system design when a planning team faces such projects. To achieve this objective, lean scheduling methods are analysed by a complex production system framework including: variety of tasks, task interdependence, supply chain interdependence, and work density. Two simulation case studies are presented. First, the finishing phase of a residential building presents the case of a non-linear project. Second, the structural works of an industrial project presents the challenges of a non-repetitive project. The main finding is that non-repetitive projects can be handled as multiple repetitive non-linear stages. However, the main challenges include the reciprocal interdependence between trade contractors, the work density disparity between locations and trades, the capacity buffer design, and production rates predictions for the assembly of one-off products. This research contributes to the understanding of scheduling in projects where the linearity assumption of activities is violated.