Those usually occur when calling something in a class that is client-side only. The same may happen for NoSuchMethodError, not tested.

Example: https://gist.github.com/SM9CC/da23ddf8c3a0edf57986ad96341c2d3d

java.lang.NoClassDefFoundError: net/minecraft/class_4587
    at Not Enough Crashes deobfuscated stack trace.(1.16.4+build.9)
    at java.lang.Class.getDeclaredMethods0(Native Method)
    at java.lang.Class.privateGetDeclaredMethods(Class.java:3244)
    at java.lang.Class.getDeclaredMethod(Class.java:2551)
    ...

This is not a bug.
net/minecraft/class_4587 is the true description of the exception. Changing it to anything else would disrupt the true meaning of the exception, and make it harder to find bugs. Furthermore, since this is just an exception description, remapping this would require a completely different system of parsing exception descriptions.
Finally, remapping net/minecraft/class_4587 is not possible, obviously, since no such class exists. Imagine that error was " class not found: shober$##&#-+#+(#" , what would you remap it to?