Some of it comes from expectation, but most of it comes from nowhere.
As far as expectation goes, we expect the Devs to follow their own standards they claim they've set when it comes to Job Balance, and discrepancies rightfully get called out, even should those discrepancies be minor in the grand scheme of things.
For example, using Reaper as that's being the topic of the thread, at the time of release, Arcane Crest violated the idea of utility vs damage. Whether or not it was too powerful wasn't the case - It was the fact that no other melee brought this capability, so as the initial scrutiny of its place in the damage meta began to sit, it becomes a glaring point of contention that you have a more flexible, more powerful, and non-offensively tied defensive utility that also benefits the party, compared to Samurai, who must use Third Eye to generate Kenki, Ninja's whose is available less often and selfish, Dragoon who gets hung out to dry, and Monk, who needs someone put the 'Oop' to their 'Alley' on Mantra.
This comes from the "expectation" that all Jobs have exactly (Using a hard number to illustrate this) 100 "points" to spend on their kit. If you take two jobs that deal the same amount of damage, then you expect that they have roughly equal capabilities in non-damage areas. The issue stems that some utilities are valued far more (RE: are more relevant to the content in question), so the final tally seems like it would outweigh another class whose utilities are not valued in said content.
Frankly we'll be doing this dance until the end of time, because while the Devs won't outright clone every job, they will adjust it enough that these small utilities will effectively be the only difference, and therefore will become even more contentious as small utilities shift in their value from each patch of the game.
Without a significant paradigm shift in their job philosophy, this is the lot they have chosen to deal with.
As for the "most of it comes from nowhere" part, a good amount of that just stems from a general playerbase not knowing what any job other than their own has been through or is capable of, and sometimes, not even then.