Kosher certification has a bunch of complexities. There are several big national certification authorities, but they have different standards, with Tablet-K accepting some things in the realm of cheese production others don't. Some small local hechshers provide more supervision then the national chains, but piggyback for the tough halachic questions.

And then there is the whole milk thing, where kashrut organizations have largely said that the FDA is enforcing the rule better then they can, so they won't bother, but some consumers don't think this is good enough.

There is also a controversy over slaughterhouse conditions brought to light when a kosher slaughterhouse was raided by the agriculture department for health violations.