In article <a5d587fb0809170303x71ebde31r8adae082b82af182 / mail.gmail.com>,
  "Michal Suchanek" <hramrach / centrum.cz> writes:

> Can I ask what character(s) that would be?

KATAKANA LETTER SE WITH SEMI-VOICED SOUND MARK for example.

This character is placed at JIS X 0213 plane 1 row 5 column 92.
http://www.itscj.ipsj.or.jp/ISO-IR/228.pdf

In unicode, it is represented by
KATAKANA LETTER SE with
COMBINING KATAKANA-HIRAGANA SEMI-VOICED SOUND MARK.

> I thought that every Kanji and Kana character has its codepoint in
> either encoding so there is never any reason to split or join
> characters while recoding into a different encoding.

It is true in JIS X 0208.  But it is not true in JIS X 0213,
newer japanese character set standard.
-- 
Tanaka Akira