Since Crystal Tokyo "fanon=canon" was brought up, I'll add one often related one: pet peeve is manipulative Pluto with the "TV of Time" instead of the "Gates of Time". For god's sake. The woman's job is to stop time travellers from abusing things, not suddenly gain the ability out of someone's ass to watch someone's entire life in fast forward and then be cold enough to kill a good person or whatever. It's total and utter -bullshit-, even beyond that of Crystal Tokyo. Manipulative Pluto is -fail-. It's not a horribly bad plot device once in a while, if just plain cliched, but dammit, fanon!=canon.
A few general comments. As a series that spans 100+ episodes, and required the use of filler material, as well as changing much of the material from the manga, are you surprised that there are plot holes in the anime? This happens with any series that goes on for long enough, and if it deviates or starts to add filler material, it's even more likely to screw something up.
Also, the only case where I tend to see "manga = canon, anime is bullshit" stuff tends to be Ranma. And people still base their fics on the anime. Actually, almost all the time, I see that the anime is prefered if the anime covers more material than the manga, even with filler. If they don't, people will still use the personalities from there or use interpretations from there.
The reason is simple. Characters have more time to get fleshed out in some fashion. While yeah, sometimes people are lazy and they are reduced to mere stereotypes by the voice actors and directors, people like to see the flawed civilian that has some sort of superpower. It's the Peter Parker Syndrome. If the character shows a certain amount of personality that doesn't quite show up in the manga, people latch onto it.
And being able to hear how a line is said has a strong effect in how a person comes across that you can't necessarily get across in a written format unless you are very good with showing that body language in the manga.
As for myself, I tend to use whichever material I'm more familiar with. If I'm familiar with both, I'll use whichever one I deemed superior storytelling. If I really liked something from the other, I'll borrow it if it doesn't contradict anything else.
I'm hardly the only person that does this.