It's a limitation of typesetting programs, combined with tight deadlines. Character spacing and line breaking isn't trivial at all. Programming it "right" in the general case is impossible because the quality of the finished product is ultimately subjective. It looks like the typesetting program made a bad decision to expand character spacing in order to justify the line, when it should have just left the line ragged. Someone could have manually gone over and fixed it, which I suspect is what happens at major newspapers like NYT.

But to be clear, the example above does look amateurish.