Bad mutations VS good mutations.

Mutations accumulate over an organisms lifetime usually without the organism "knowing". They may even be passed on to future generations if the mutation happened to occur in germline cells responsible for generating gametes. This is what lends to different alleles of the same genes -- variations in skin color/eye color is an example. What dictates an alleles usefulness is if it promotes reproduction and survival based on the environment in which the organism inhabits. Because the environment is really slow to change, we rarely see the benefits of any mutation in human beings.

But certainly the negative mutations are easy to flag, and hence anything that isn't that must be ok?

You could say that. Many spontaneous abortions (miscarriages) are said to be due to errors in the DNA either from conception or in the gametes themselves. I don't know how they confirm these, but it is certainly something to consider when making such a statement.

That is an interesting point.