Doctrine proxy class files can't be overwritten by other SAPI type
When you run FLOW3 with empty caches for example from the command line, Doctrine proxy classes will be created. However, these files can't be overwritten or trashed by FLOW3 when it's running in web mode because the files are created with read-only permissions for the group. The same happens vice versa (first hit with Web).
The solution would be to create Doctrine proxy files with