Adding buildscript dependencies in top build.gradle?

I have just had problems with buildscript dependencies.
In the top build.gradle some jars was added to classpath.
Later I added a plugin in module. To my surprise the top dependencies had priority over the buildscript in the module. I got several MethodNotFountExceptions before I started to figure out that it could depend on previous added dependencies in the top level build.gradle.

Is this a known problem/anti pattern?

It is known, but not a know problem but expected.
The buildscript classpath of a project is in a class loader.
The buildscript classpath of a subproject is in a class loader.
The parent project’s class loader is a parent of the subproject’s class loader.
And due to normal class loader rules, classes from parent class loaders take precedence.