A (master) thesis about the development and assessment of an algorithm has some limitations. The method chapter is organized as follows:
The algorithm itself is not optimal and potential flaws exist in some modules. The simulated scenarios were selected in order to create a representative assessment, but are not covering the entire range of possible conditions. The evaluation method is based on a number of simplifications which might lead to faulty final results.
To make sure it doesn't seem like I'm hiding something, I would like to describe all of these limitations. Where would this fit best? In the individual sections of the Method chapter? Could I title the chapter after methods "Results and Discussion" and mention it there? Or in the conclusion?