Methodology is a set of methods and procedures describing how to reach a result. Every enterprise developing products or services makes use of various development methodologies  but they are sometimes diverted from their original intent, for example for project management  purposes.
As for projects, the application of methodology produces “deliverables” , for example specifications documents like customer requirements, functional analysis, high level design, etc. These documents are sometimes used as a mean to measure the progression of the project; their presence being the signal that a project phase is completed, that a project milestone  is reached.
But what happens when the specification documents content changes or evolves ? What is the impact of these changes on the project ? Does it mean that the project phases that were completed aren’t anymore and that we go round in circles ?
The reality is such that specification documents often change because the customer needs evolve over time or e.g. because an “agile”  development methodology is being used which is iterative and incremental by nature. In each of these cases the specification documents evolve during the project lifetime, consequently using these methodology deliverables as a measurement of a project progression is not ideal.
In such situation, the major side effect is to implicitly and indirectly promote a “waterfall”  development approach which is less compatible with an agile approach aiming at addressing better and faster customer needs.
An additional factor reinforcing the waterfall approach derives from the deliverables lifecycle; each document update must be approved by all the project stakeholders: customers, product manager, third parties, developers, … Constantly re-approving the same documents may induce the impression in the minds of some stakeholders less literate about “development methodology” that the project is not progressing well. They are consequently more reluctant to approve this nth version of the document and tend to push towards a stabilisation of its content.
In conclusion methodology cannot be substituted to project management tools and deliverables must not be confused with milestones. It is the project management toolbox that must be adapted to the characteristics of the chosen development methodology.
 Software development methodology, Wikipedia
 Project management, Wikipedia
 Deliverable, Wikipedia
 Project milestone definition, BusinessDictionary.com
 Agile software development, Wikipedia
 Waterfall model, Wikipedia