Yes the problem with “whataboutism” is that it can be used to dismiss any claims of double standards without further examination.
For example, here in the US we punish black murderers more harshly and more often than we do white murderers. If a black murderer tries to point out this double standard, their claims would accurately be dismissed as “whataboutism”. But when you view the system as a whole, then you can see that systemic racism is undeniable.