Xcode broke YouCompleteMe error highlighting

I was working a project in C++ and all of the sudden my Mac said that Xcode was finished updating, so I just exited out of the popup and didn't think anything of it. I went back to my project and tried to run my makefile and it said I need to be root to accept Xcode's terms. So, I just booted up Xcode, accepted the terms, and quit. Now, when I work on my project in Vim, I am getting all kinds of errors. E.g.

#include<iostream>  // 'iostream' file not found
#include<string>

int main()
{   
    std::cout << "hello" << std::endl; // use of undeclared identifier 'std'
    return 0;
} 

I have no idea what has happened. Can anybody help me?

I use g++ to compile and this is the output of g++ --version:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-    include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.3.0
Thread model: posix

My Xcode version is now 6.0.1.

All this being said, I still seem to be able to compile my code. I am just getting all types of errors in Vim, related somehow to this Xcode update.

I use YouCompleteMe for error highlighting.