The fixincludes script interacts badly with automounters; if the directory of system header files is automounted, it tends to be unmounted while fixincludes is running. This would seem to be a bug in the automounter. We don't know any good way to work around it.
The fixproto script will sometimes add prototypes for the sigsetjmp and siglongjmp functions that reference the jmp_buf type before that type is defined. To work around this, edit the offending file and place the typedef in front of the prototypes.
There are several obscure case of mis-using struct, union, and enum tags that are not detected as errors by the compiler.
When `-pedantic-errors' is specified, GNU C will incorrectly give an error message when a function name is specified in an expression involving the comma operator.
Loop unrolling doesn't work properly for certain C++ programs. This is a bug in the C++ front end. It sometimes emits incorrect debug info, and the loop unrolling code is unable to recover from this error.