Fail to reproduce results in a published paper. Is this an academic misconduct?

Academic misconduct is the last thing you have to consider, not the first.

First, you have to consider that there might be something you are overlooking (e.g. an updated version of the code, or the data set is not really the same, or something related to the machine or etc.). Then, you have to consider that mistakes happen, and as I wrote in this answer, yes, there are plenty of errors out there, that do not come from academic misconduct: a mistake can have leaked somewhere in the paper, code or graphs.

Therefore, if you have reasons to consider that difference significant, you can contact politely the authors trying to set up a scientific discussion -- not an accusation -- to understand where the difference comes from.

You seem to want to head immediately to the worst case, and a fairly serious allegation. Data manipulation and academic misconduct are very serious things. And starting off from that position is pretty antagonistic and is likely not going to be very productive in actually figuring out what's going on - more likely, it's going to get everyone defensive.

The first thing you should do is email the authors with a clear, detailed account of what you did in your replication attempt, and where the differences you found from their results are. Ask them if they might be able to provide more details on their own methods, or review yours to see where they differ. There's any number of ways a replication based experiment can subtly deviate from a published work.

Even if the answer is "No, we can't account for that", it may very well be human error, rather than misconduct. But before you can even go down that path, you need to make sure it is a genuine replication failure.

If the result proposed by the published paper depends on some sampling of data, then a probable sample error could be introduced. This would mean you would have to follow a Test of Hypothesis to disprove their result.

Edit addressing the added details:

Variance of a population is surely equal to or larger than its subset. You cannot accuse misconduct purely on this case. To reject their claim of a mean, median, or variance, you ought to do so with a formal test of hypothesis taking your own subset into consideration.

There are several standard materials available on test of hypothesis. For a quick reference, you may refer my concise expository paper here.