Fire the canon (out of a cannon)

There is no such thing as canon. Canon does not exist. It is a hallucination. A bad trip.
No story is consistent. No story can be consistent, for the simple reason that the human mind cannot construct a world inside itself. We can only construct a series of images. If they are good enough, the reader's imagination will create her own images to connect the images we wrote.
Every reader constructs her own interpretation of our story.
Every story is finite. Every interpretation of a reader is also finite.
A world, an actual world, is infinite. Therefore, no amount of details will cover everything. There will always remain empty spaces for inconsistencies and plot holes.
It happens to authors who labor for decades, building and improving their secondary worlds. Tolkien created entire language families, and Tolkien forgot about the eagles. And it doesn't really bother us. Just like that, we take a part of the canon and either explain it away or ignore it.
If it can happen to Tolkien, then surely it can happen to a cartoon series which exist to sell toys and where different episodes are written by different authors.
MLP:FIM is inconsistent, yes. Like every other story in existence. It should not bother anyone. Especially not fanfic authors who write stories based on a cartoon series which isn't even finished yet.
There is no such thing as canon and non-canon fanfics, because there is no such thing as canon.