The PhD contains a training part that has to be filled with following courses. Generally, this will be split into a set of courses about the field of your research, and more general courses focused on obtaining transferable skills (such as language courses, presentation and writing techniques, etc.). It is important to have a clear agreement with your promotor at the start of your PhD about which courses you will follow, and write this down in the training and supervision plan.
Many graduate schools offer the opportunity to follow courses. Sometimes these courses are not sufficient for the PhD candidate. In that case it may be interesting to look for graduate schools that do have such a specific course for the candidate. It may prove to be difficult to find graduate schools that offer courses. On the website of the KNAW you can find the acknowledged graduate schools in the Netherlands.

Of course you don’t have to limit yourself to the Netherlands while finding courses. On this and this website you will find links to many graduate and PhD programs all over the world. At these graduate schools, courses can often be taken by students from outside the graduate school.