What to do when you're cited, but the author doubts the validity of your results
So your study was (by design) limited in scope, they're researching something outside of your scope, and your approach fails to provide a solution in their problem area.  It sounds like you and they agree.

Take a close look and see whether they actually said that your study was compromised, or whether you simply got defensive because they said your method failed when they tried to use it.

Your discomfort may be caused by the fact that you've failed to look at it from the perspective and scope of their paper.  They have to prove that there's a problem, and that existing approaches (including yours) don't solve that problem, because that motivates the solution they present.  If they aren't making any claim that your approach doesn't work within the scope you claimed, then while you may have preferred that they used verbiage such as "Our problem is excluded by the approach described in user67334's groundbreaking work on (other problem)", they didn't.

Instead they used words which are descriptive from the perspective of the problem they're discussing, and since that's a limitation you already explicitly acknowledged, doing so doesn't actually detract from your work in any way.