One of the most common mistakes is not recognising that tools are just that and as such you need to pick the correct tool for the project you are working on. Not to be blindly led by the methodology that you have just learned/is flavour of the month.
I know I did that quite a bit when I started out, thinking a new tool was the silver bullet I was looking for and not recognising that I just needed to pick the correct tool for the job at hand, and that is truly only something that comes with experience (at least in my case ;-)).