Version: 2.1b4 (using KDE 4.5.2)
When using "Apply word wrap" at a text, lines that contain comments are simply wrapped, instead of new comments are inserted for the wrapped comments.
Same/similar problem with math environments like "$$ a < b$$", in case of a wrap of such an environment, it is not closed correctly anymore.
The problem with word wrapping comments is tracked in bug #105373.
For the problem with "$$ a < b$$", do you mean that a word wrap might turn $$ into $<new line>$ ?
*** This bug has been marked as a duplicate of bug 105373 ***