So since incorporating in 1851, let's say they put out 60,000 issues. 1 issue would represent about 0.002% of their output. How do you get to over 5% wrong?

It's a spot check. They checked one article from one of those issues and they spotted an error, so odds of >5% wrongness are high in their view. (They need a larger sample size and some statistics to make such a claim, but certainly your numbers are way off, but in the other direction.)