My advisor cited her colleague's papers in her own methodology even though she did not use those methods. Does this qualify as scientific misconduct?
The issue here is not citation, it is correct reporting.  If a method varies from the cited version, the appropriate thing is to say something like &quot;Method from FrozzBozz et al.[73], modified by change of RPM from 3000 to 6000, growth media from LB to M9, and phase of the moon from new to full.&quot;
But did the method actually differ?
Now, there are definitely arguments to be made about the level of detail that is necessary and appropriate in protocol reporting.  For example, the details about how a sample is shaken may or may not matter, but are often omitted because people are often simply not very systematic about this.  Likewise, layout of samples on a 96-well plate is typically not reported, even though there are sometimes locality effects. Thus, many of the things that you are concerned about might be reported by one group but not by another.
The key distinction between reportable and non-reportable method details is whether a reasonable reader might expect them to have a significant impact on outcome.  In many fields, this is more clearcut: for example, an algorithms paper reporting the number of iterations required to solve a problem would not declare the system the algorithm is run on, but one reporting the time of execution would.  In biological sciences, however, it is often quite unclear and reasonable people have very different perspectives here.  Thus, the Ph.D. candidate might not even believe that they have meaningfully changed the method at all!
My advice it to start by approaching it from this perspective, in a non-confrontational manner.  Start by just asking for help in understanding the differences in method.  If they do not explain in a way that makes sense, then it would be appropriate to escalate to the PI that ultimately supervises both of you, and ask for help in figuring out what details of method variation are appropriate to include.  No need to get into accusations of lying at this stage, and you both might end up learning new things in the process.