I have a java project with two src directories.
The first srcA contains a class file com/pippo/pluto/A.java, the second srcB
contains com/pippo/Pluto/B.java.
The project cannot be compiled because the same resource is found (packages
com/pippo/pluto, com/pippo/Pluto)

So why do you think that this is a bug?
The file system doesn't allow us to create 2 directories with the same name but 
different case.
You need to change one of the names.

java is able to handle package that differs only for cases, that should be
supported by eclipse jdt core too, else it is not fully compatible with java
compiler.
that is not a blocker ticket because there are some workarounds, like create two
dependent java projects, then eclipse works fine without errors
what do you think ? ;-))

>The file system doesn't allow us to create 2 directories with the same name but 
>different case.
they are not in the same fs:
project
   srcA/com/pippo/pluto/A.java
   srcB/com/pippo/Pluto/B.java

This isn't a JDT core limitation.
No Java compiler successfully compiles this code because we all receive the 
same error when we try to write out the .class files.
The .class files are written to the same output folder. That is where the 
collision occurs.
You can configure your source folders to have their own output folders, but you 
should seriously consider renaming one of the packages.