Here's a MWE with LaTeX2e, classicthesis latest version, using footmisc.
footmisc itself does not cause the problem.
\documentclass[final]{book}
\usepackage{classicthesis}
\begin{document}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with one digit}
\footnote{Footnote with two digits} % "0" and "F" may overlap here.
\end{document}
The problem comes from the negative length set for \footnotemargin
with the flushmargin
option.
The following patch fixes the problem.
--- classicthesis.sty.orig 2018-04-02 00:33:02.689565353 +0200
+++ classicthesis.sty 2018-04-02 00:33:14.857564987 +0200
@@ -594,11 +594,9 @@
\deffootnote{0em}{0em}{\thefootnotemark\hspace*{.5em}}%
\message{Using KOMA-command "deffootnote" for footnote setup}%
\else
- \PassOptionsToPackage{flushmargin}{footmisc}%
\RequirePackage{footmisc}%
- \setlength{\footnotemargin}{-.5em}%
- \PackageWarningNoLine{classicthesis}{Using package "footmisc" with option %
- "flushmargin" for footnote setup (not 100\% the same as with KOMA)}%
+ \PackageWarningNoLine{classicthesis}{Using package "footmisc" for %
+ footnote setup (not 100\% the same as with KOMA)}%
\fi
% ********************************************************************
Thank you for pointing to this problem and providing a solution. Changing to the
marginal
option is another possibility which is a bit closer to our KOMA-approach from its appearance.\PassOptionsToPackage{marginal}{footmisc}
The fix will be in the next release.