I run into this quite a bit. It might be with other tags as well, but it looks like files that include <a...></a> tags don't want to beautify (Tools > Beautify All Files) in the Editor. Nothing seems to happen when I try. Is that expected behavior?
The following is a Scrambled version of part of a book I'm messing with right now. Supposedly, it's been beautified. But, the heading and paragraph don't even get indented. Just removing the leading <a> tag pair lets the indentations happen.
Code:
<a id="GBS.0245.01"></a>
<section class="aboutauthorpage">
<h2><span epub:type="pagebreak" id="pg_2" title="2"></span>Zqpsi zhs Cn*jmxp</h2>
<p class="center"><img src="../images/epub_Scalzi_2016_no_cr_fmt.jpeg" alt="Photo of John Scalzi" class="imgsetwidth"/><a id="GBS.0245.02"></a></p>
<p><a href="http://us.macmillan.com/author/johnscalzi?utm_source=ebook&utm_medium=adcard&utm_term=ebookreaders&utm_content=johnscalzi_authorpage_macdotcom&utm_campaign=9780765388926"><span class="smallcaps">Yxty Tojzak</span></a> pf evu xd okf moam nae*k*qhk vzs di*uaticmp BC ik*wwauq vo yywwat xh thk qgvi dncwuj. Vzs ilz*nbrajs xcl*efmk*jyg oy*wqa, <i>Bmc Aab’v Bgl</i>, qir rgx dco*ijqq sqf*wson’e Ndoo Z. Zdjg*hdun Elzvn cym Lnvn Ktj Ncsmze. Lxj <i>Hkx Zqfo Krbbk</i> jibv*bacwssn bs*dyzsn <i>Wjx Wzrf Ebpmjq; Qgxyr Pw*piwv; Ark*ffrsmi</i>, gkyxt bct 5372’y Ybsv Bvofl isp Sbsk Uaise; wnk <i>Ctkm Xo</i>. Ql*cy*gzqy nsiv lhb uoehbm wmnc qcap, <i>Izen*idyk</i> (<a href="http://whatever.scalzi.com">mpan*mctr.vdbmmh.rnn</a><a id="GBS.0245.03"></a>), pgi oqeb sdgcnr oyr hwi scvom Kvbh Icaphd. Bk taobr ps Wfbk mtnf qfy sqoy anj upaco*ywl. Ysw tda gcno mh ckz bzekb jn*saewk <a href="http://us.macmillan.com/authoralerts?authorName=johnscalzi&authorRefId=1351591&utm_source=ebook&utm_medium=adcard&utm_term=ebookreaders&utm_content=johnscalzi_authoralertsignup_macdotcom&utm_campaign=9780765388926">beci</a>.</p>
<a id="GBS.0246.01"></a><a id="GBS.0246.02"></a>
</section>
</body>