How to identify a research question as artificial
While it's hard to know without knowing all of the specifics, it seems likely to me that this criticism is similar to saying that the questions are poorly motivated.

There are an unlimited number of research questions that might be asked. Why are these the ones that are interesting?  Consider that in many cases, a specific research question may be seen as a "natural" consequence of the underlying motivation.  

For example, if one was studying cancer and noticed that a particular group of people got cancer much less than expected, the "natural" research questions might include whether they have different genetics or different habits or whether this is related to other known modulators of cancer frequency, or whether other groups of people with related characteristics can be predicted to have different cancer rates.  All of these might have obvious interesting consequences for the understanding and management of cancer.

An "artificial" question, by contrast, would be any question for which no such clear narrative is available.  It will be at least partially a matter of perspective, but rather than debating whether a question is artificial, it would be good to examine whether it is really well motivated. If so, explain the motivation better.  If not, get a more interesting question.