I think most people who answered are a bit clueless and have found a solution by trial and error. I too had this issue recently and looked at the various solutions in this thread and they did not make much sense. I looked in to my project's makefile (it is handmade by my project lead) and I found -j11 in there. I replaced that with -j1 and it fixed the problem. The hunch was that make was probably doing a bad job at running multiple jobs (threads) i.e. while one thread was working on a file, another thread was trying to use it.
For those who use an IDE to compile your code, you need to look for a build property where you can set the number of jobs and then try compiling your code with the number of jobs set to 1. You might also have to close and restart the IDE (it all depends on how the IDEs are programmed).
I understand that this might hinder the performance of your builds but there is probably no alternative to this until either make fixes this bug (if there is one, I haven't bothered to dig in) or the makefile generators become smart enough to prevent this situation.