I figured this was inevitable when jobs started using 32bit large primes. The code choses quadratic characters from the primes larger than the largest factor of the algebraic sieve values. When you allow 32bit large primes, there is a danger that some of the quadratic characters will overflow the 32bit size and wrap around to the smallest primes.
This isn't a fatal error, it just means that any quadratic characters that wrap around will be useless during the linear algebra. As long as you get 57 characters that don't do that, it should be enough for the square root phase to work correctly. If you see that warning a large number of times, you may have to modify the code and rerun the matrix building step.
