If I understand your problem correctly, you don't want approximations as given by vpa. In that case, here's the best advice I can give without seeing your inputs:
Don't use calls like sym(5^(1/2)) (although that particular one works just fine), use sym(5)^(1/2) instead.
If you say, e.g., sym(5^(1/3)), that will be the same as saying sym(1.709975946676697) and will not magically detect that you meant 5^(1/3), not 1925261759066421/1125899906842624. I.e., if your input contains sym(5^(1/3)), it contains a rational number with large numerator and denominator, which will show up in the output.