Now these errors are for the most part irrelevant in most applications, because food for example is still very edible and nutritious even if it is not absolutely 100% as good as the original, same goes for most spare ship parts and such.

Star Trek's replicators also modify the food, which may matter more than small-scale errors. They specifically create a copy of the food that is deliberately nutritionally tailored for your specific dietary needs, and to remove poisonous substances within it.

Those errors tend to be more of a problem for big complex molecules like DNA, or sophisticated things like computer chips.