Most if not all of them are real issues that mediawki helps hide from users and readers. For instance, a good number of them relate to the poem extension, it creates a <div> but sometimes users wrap that around a span for strange reasons, (<pages index="Historia general de la medicina en Chile, tomo I.pdf" from=24 to=25 />):
<ref name="araucana"><poem>{{bloque centro|<center>CANTTO XXII</center>
Vimos allí del lince preparados
</poem></ref>
That expands to something like this:
<span class="mw-cite-backlink"><a href="#cite_ref-araucana_1-0">↑</a></span> <span class="reference-text"><div class="poem">
{{bloque centro|<center>CANTTO XXII</center><br />
<p>Vimos allí del lince preparados
</p>
</div></span>
Then there is (<pages index="Gramática teórica y práctica de la lengua castellana.pdf" from=41 to=42 fromsection= "Capítulo II" tosection="Capítulo II"/>):
{{bloque centro|
<poem>
Verdad es ¿Qué ha de hacer ''una''?
::::{{d|(Tamayo y Baus ''La Bola de Nieve.'')}}
</poem>
}}
Which expands to something like this:
<div class="mw-parser-output"><div style="display: table; margin-right:auto; margin-left:auto;width:auto">
<div class="poem">
<p>Verdad es ¿Qué ha de hacer <i>una</i>?<br />
</p>
<span class="mw-poem-indented" style="display: inline-block; margin-left: 4em;"><div style="text-align:right;margin-right:">(Tamayo y Baus <i>La Bola de Nieve.</i>)</div></span>
</div>
</div>
</div>
Note how there's a div inside a span. It is possible to "fix" all of these by using workarounds. Of course adding a poem inside a reference is definitely a user error. References are designed to only hold <span> like stuff, e.g. <i>, <b> , etc. Adding a <poem> or <div> inside it causes problems as discussed in this thread (https://phabricator.wikimedia.org/T49544).
While errors could be generated whenever editors try to use these, chances are that it would upset a lot of users, so developers seem to have chosen the greater evil of letting internet browsers deal with invalid html documents. In some cases it means that users will see different rendering of the same page on different browsers.