It will be less of a problem in the future, but a lot of the versions of classic fonts floating around have funky kerning. Neue Haas Grotesk is the first properly digitized version of Helvetica, for example.
I agree, and there will always be bad digitizations or just bad fonts. My practical advice is mostly that if you find yourself having to kern more than one or two pairs you're better off finding a better typeface.
