Difference between the problem a paper is trying to solve and primary research questions it tries to answer?
As the saying goes,


  There's more than one way to cook an egg.


In the research context, this means that sometimes a problem is presented, but there are numerous ways to approach the larger problem. It's possible - in fact, it's likely - that most large problems are addressed from multiple angles by different papers.

As a concrete example (in computer science), consider the problem of sorting a list of integers. There are many, many different ways of doing this (some of which you probably don't want to use), but the assumptions you make have a major impact on how you solve the problem. So a single problem might lead to many research questions:


How do I sort a list of random integers?
How do I sort a list of integers of unknown size?
How do I sort a list of partially-sorted integers?
How do I sort a list of integers with no worse than O(x) performance, where x is some upper bound?


And so on. Each of these research questions is just a smaller, more digestible piece of a larger problem. But because the problem is so large, you can't answer every question in a single paper -- hence, the discrepancy you pointed out.