By the former I mean problems and by the latter I mean the use of issue as a widespread euphemism for problem, or as a vague abstraction that substitutes unhelpfully for clear thinking and straight talking.
When issue denotes a subject under debate or discussion, it is a convenient term, and there are certainly instances when it cannot beneficially be substituted by stronger and more concrete phrasing. That said, it seems to be widely overused and misused.
For example, instead of someone saying I dispute that or I have a problem with that, there is a tendency to soften the language: I have issues with that, I would have issues with that, There are issues surrounding that, and so on. These three examples are phrased in a way that distances the speaker or writer from their supposed opinion; consequently, their point (if they have one) loses force and clarity. My advice is to use the term sparingly and judiciously.