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Yo catalogers...
...what are the biggest problems you see in cataloging manga today? Looks like I'm writing an article with a cataloger about that very subject, and I'm bringing the manga knowledge, and he's bringing the cataloging knowledge. But that's the question he posed to me, and as I am complete pants at cataloging, I thought I'd ask around.
I do know that determining whether something is appropriate for a younger or an older crowd can pose a bit of a problem, especially if it's a series and the youth-inappropriate material doesn't show up until a few books in.
I do know that determining whether something is appropriate for a younger or an older crowd can pose a bit of a problem, especially if it's a series and the youth-inappropriate material doesn't show up until a few books in.

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Yu-Gi-Oh has three sub-series and has volume titles. Some volumes index primarily under the volume title so that one has to squint at the cover image in order to tell to which sub-series the volume belongs. Basically, somebody cataloged some volumes as a monographic series rather than as a limited run serial. The monographic titles matter because they're part of how people differentiate volumes, but the series and volume numbers matter much more. (From what I've been told by friends, this problem has been worse for U.S. published graphic novels. For a long time, there were screens and screens of titles that read, unhelpfully, 'Batman' or 'X-Men' with no other identifying information.)
Full Metal Panic and a few other series show an acquisitions problem that may not be spotted until cataloging. My library has all of Full Metal Panic except v.5. They have v.5 only of Full Metal Panic Overload. I strongly suspect that the volume of Full Metal Panic Overload was mistakenly ordered to replace the missing volume in the other series. It's cataloged correctly, but I don't think anyone ever mentioned to the collection manager that it's not what was probably wanted. There's a similar problem with Lagoon Engine. The library has v.2-3 and then has v.1 of Lagoon Engine Einsatz which is a different series altogether.
Titles with odd symbols would also pose a problem. The various .hack//Sign series and Ranma 1/2 can be frustrating for patrons to search.
I suspect that there are also questions of where the volume numbering goes in the record. Patrons might prefer to have the numbering as part of the indexed title so that they can search, for example, Naruto 22, rather than paging through a list of every volume of the Naruto manga and anime until they find v.22 of the manga. I know that, again in the local OPAC, some series list in the index in volume order while others don't. When a series runs thirty or forty volumes, that jumbled order becomes frustrating.
Hm... Anything else...?
One woman at the circulation desk commented on how many manga titles came up in her searches for things related to queer studies. My impression was that she'd filtered them out without too much trouble, but she found it odd that they came up. Not necessarily a problem but still something to be aware of.
I don't know if this is an issue with purchased cataloging records, but I've noticed that the pseudo-cataloging records pulled from Amazon often omit the author or list a translator as the only author or list only the artist or only the writer. Purchased records for manga may need more careful going over for detail than purchased records for standard monographs.
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I've also seen some fairly wonky subject fields--one volume in a series have a 650 for "High school students--Japan--Fiction" while the next will have "High school students--Japan--Comic books, strips, etc.", which might throw off search results in the OPAC. Though it sometimes gets used in a 655 for genre/form, there's no established heading for manga as a format; it's a topical term under the "Comic books" heading.