Note: I do-not follow the LaTeX community and development, most of what
I comment here is my own experimentation and answers and references made
by people answering to others in LaTeX-related support websites. Please
let me know if you find solutions that fix this problems (and the ones
mentioned in references) without needing to apply multiple fixes for a
single document.

First one must understand how TeX and LaTeX work (or how they don't work
in some cases). Basically, these two are awesome as long as you don't:

1. Depend on wraped elements, like:

Parapgrah text could start here and so continue in next line,
and so it goes this way until all              [ Some other   ]
text is inserted here, without need            [ element here ]
for much scripting, calculation, or complex setups.

   a. Note for item 1: "Element" can be text, image, table, and any
      other thing. 

2. Mix multi-column texts (or paralel-column texts) with single-column
   text and frames or lists between the columns. Like:

a. First.   c. Third.
b. Second.  d. Fourth.
e. Fifth.
f. Sixth.       [ Framed list and ]
g. Seventh.     [ this paragraph. ]
h. Eighth.      [ a. First.       ]
i. Nineth.      [ b. Second.      ]

3. Depend on content-aware list balancing inside multi-column
   text. Like:

a. This list would...           c. as the sole member of...
b. probably have item d...      d. column two.

4. Depend on table headings reappearing if the table is broken in
   multiple pages (using "longtable" package probably). It works as
   expected if you do-not depend on such headings reappearing.

All of this is important to avoid, also considering that there might be
other things that I forgot.

Now for a detailed explanation of why each item don't work well, and
what to do instead (my own suggestions):

When TeX was made, it was made in such a way that even with limited
resources, documents could be made, and it assumes some oddities to make
sure of that (as can be seen in [[http://youtu.be/jcY1zLJNqX0]], from
07:30 to 12:33, from more simple explanation to more advanced
explanation of the assumptions and consequences).

So, as my own suggestions, set documents that all non-text things (or
framed text) are displayed in other pages of their own, or in the next
paragraph where it was referenced (but do-not force it to display in the
sides. Stay with same colums throught the entire document, specially if
the involved paragraphs have lists of some type (like itemization,
enumeration and description lists).

As an addendum: For taking notes of things (even while I'm in collge, so
that I can take notes using mobile devices) and for organizing my life
and agenda, I use Org (Org mode in Emacs, or MobileOrg for mobile
devices), not LaTeX. I prefer Org because, by using GNU Emacs with Org,
I can export my texts to other formats, including LaTeX or even PDF
(passing through LaTeX), and it even allows me to use a mix of LaTeX
inside, and also allows me to use spreadsheets, do some graphic
plotting, and use any other language I have enabled for use inside some
special blocks.

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