Is bad writing an acceptable answer to questions when they are about shoddily written events?
Yes, if you can elaborate on why it is a plothole, as opposed to it just being a confusing event. As Memor-X mentions in the comments, explaining why it is poorly written, be it due to bad translations, multiple authors, or alternative endings, would make for good elaboration.
If so, is there a way to safely identify bad writing?
This is a tad harder, but somebody knowledgeable about a franchise as a whole (familiar with several of the stories mediums) should usually be able to tell confusing and/or plotholes apart from each other, just as well as they can differentiate between cannon/non-cannon.
"Are manga and anime, by principle, poorly written?" By principle? No. The problem is that there is a lot of crap out there, just like every other medium ... If there is a problem with anime and manga, it is that the internet has made it very easy to put every new show and manga under the microscope, meaning that we have to wade through more crap than in other mediums. However, that's not a problem with the medium itself.
- Are anime/manga poorly written by principle
Light Novels not only would fail according to the Hemingway App (which redlines your text based on Hemingway’s style), and Stephen King’s advice in “On Writing”, but are very intensely modern, in the sense that they put the individual at the center. Well, time to break that down.
- Light novels are poorly written and adapting them shows that
So besides being knowledgeable there is no 'easy' way to identify bad writing within anime, manga and it's related mediums. As they often diverge from the well known literature standards.