Transitive dependencies not found
One common example is when transitive dependencies are not met. More often than I would like, I get into the problem of transitive dependencies of one of my dependencies cannot be found. Latest one was when using CXF, where it failed on finding some JAXB dependency in some specific version.
You could argue, that this is not mavens fault, but the fault of those deploying into the repository. But it appears to happen so often. Why is this? Maybe because it is too hard to do deployment correctly into it.
All the site/report generation crap
From the start, maven has taken on the role of building more than just our sources. With the reports and site plugin, it can generate documentation in html-format from various sources. It can also produce various reports and integrate them into the generated site.
Nice, but... It takes ages to process. It outputs a big load of crap when running, which hides actual problems it might notice on the way. The syntax to write the documentation sources in (xdocs, apt) are crap.
Why not just document on a wiki. Hey! People are already doing that all-over.
When dependencies clash
This can occur in many different forms. One example is what Jacob writes about in "A badly packaged project will break builds". The essence is, that transitive dependencies explodes in complexity. Some project might depend on spring-web-2.0.5 as a fine-grained dependency and another might depend upon a spring-2.0.4, which is a "all of spring" dependency. These are in different versions, and might clash and be incompatible. And maven cannot know what to do about it. It cannot even notice, as the artifactIds, "spring-web" and "spring", are different.
It is nice to be able to just depend on something declaratively, and automatically get a load of needed transitive dependencies with it. But, it is like pissing your pants. It warms right when you are doing it, but it quickly gets cold.
I think the whole dependencies problem is inherently complex. And very hard to put into a build tool for automatic management.
So, what to do?
Sadly, I have no really good advice on what to do then. I know for sure, that I cannot do better myself.
Sometimes, I wonder how far we could come, by doing our builds with: