I'm bashing the act, not Apple. You cannot take what's not yours and Corps have a history of this, perhaps you can studies history and maybe you'll see. I've seen these actions for many years and this is not Apple's first case.
However, "you can't take what's not yours" isn't always true and this gets even worse when your not talking about objects but ideas. How do you "own" an idea? Do you write it down and boom it's yours? Do you have property of it? The usual legal concepts are fuzzy when applied to Intellectual Property. IP disputes are complex because the subject matter is itself terribly complex. Hundreds of cases each year go through courts all over the world over such questions and I can assure you, saying "But it's mine! You can't take it!" is hardly ever enough.
If you file something wrong, you have to bear that burden. Why is it so strict? Because records should be trusted by those who consult them. If the record says it's owned by a company that doesn't exist anymore, this info is to be trusted, even if reality is slightly different. Especially in the US, such requirements are very strict. If your filing isn't valid, then you've never had any exclusive rights to your idea. It would be exactly the same if Apple for some odd reason filed a patent for "Apple LLC" instead of "Apple Inc.".
With that in mind, it's easy to read the story differently (and in that respect, it
is one-sided) : Apple wanted to use Animoji, checked the records, saw one but it was void. They asked to buy it, the guy said no, so they used the options the law grants them. And they
will settle and that developer who hasn't been actively developing that app will be quite content (and his lawyers too, I'm sure they took his case only for the contingency fee). Maybe if the filing were actually correct, things might have been different, but Apple would have bought anyways.