They can interpret anything sufficiently vague as they see fit. For example Article 10 of Directive 2004/38/EC states that a government shall only require "a document attesting to the existence of a family relationship", which most people would consider to be a marriage certificate, it also states the residence permit will be granted within 6 months of presentation of the documens. Article 25 limits the cost of the issuance of the residence permit.

Unlike many EU countries, the Netherlands requires that the marriage certificate is "legalised" and charges for the process. They will not even accept the documentation before you go through this extra legal procedure thereby increasing the total time to over 6 months. Under some interpretation of article 10 and 25, this would be illegal, they have a different interpretation.

You can find various compliance studies for directive 2004/38/EC and other directives as well. It is just a fact in Europe that the transposition into local law leads to inconsistent application of the law. Applying for the same visa (from the European perspective) in the Netherlands and in Germany can be two wildly different experiences.

Not true. Many of the directives differ in countries (even major ones - for example countries in EU that don't use Euro). EU wants people to believe it is USA but it is not. The directives are not enforceable directly but if you want to be good EU country (which has its benefits) then you need to behave :)