I'm having an "strange" problem when compiling a document made of different chapters. I use this code in the main file:
\include{Capitulos/01Introduccion}
\include{Capitulos/02Metodologia}
\include{Capitulos/03ClimatologiaSST}
\include{Capitulos/04Modelizacion}
\include{Capitulos/05Conclusiones}
Then when compiling an extra page with just an F appears after chapter 3. I thought it was because the chapter ended with a long table but when table is removed the problem also appears. Then I removed chapters 4 and 5, chapter 3 is then just before the appendix, and then the page with just an F disappears.
Any hint will be appreciated.

EDIT
main aux-file:
\relax
\catcode`"\active
\catcode`<\active
\catcode`>\active
\@nameuse{es@quoting}
\catcode`'\active
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand\HyField@AuxAddToFields[1]{}
\@input{Cascaras/cover.aux}
\select@language{spanish}
\@writefile{toc}{\select@language{spanish}}
\@writefile{lof}{\select@language{spanish}}
\@writefile{lot}{\select@language{spanish}}
\@input{Cascaras/dedicatoria.aux}
\@input{Cascaras/agradecimientos.aux}
\@input{TeXiS/TeXiS_toc.aux}
\@input{Capitulos/01Introduccion.aux}
\@input{Capitulos/02Metodologia.aux}
\@input{Capitulos/03ClimatologiaSST.aux}
\@input{Capitulos/05Modelizacion.aux}
\@input{Capitulos/06Conclusiones.aux}
\@input{Apendices/01Rams.aux}
\@input{Apendices/02MapasSinopticos.aux}
\@input{Apendices/03MapasSST.aux}
\@input{Cascaras/bibliografia.aux}
\@input{Cascaras/fin.aux}
aux-file of chapter 3
\relax
\citation{Bethoux1999}
\citation{Vargas2010}
\@writefile{toc}{\contentsline {chapter}{\numberline {3}Climatolog\IeC {\'\i }a de la temperatura superficial del mar}{33}{chapter.3}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{cap3}{{3}{33}{Climatología de la \tsm \relax }{chapter.3}{}}
\newlabel{cap:climatologia}{{3}{33}{Climatología de la \tsm \relax }{chapter.3}{}}
\citation{Millan1995,Pastor2001,Estrela2003,Lebeaupin2006}
\citation{Nykjaer2009}
\citation{Rixen2005,Salat2002,Santoleri1994}
\citation{Ortenzio2000}
\citation{Marullo2007}
\citation{Kilpatrick2001}
\citation{Gentemann2003}
\@writefile{toc}{\contentsline {section}{\numberline {3.1}Datos de temperatura superficial del mar{} y metodolog\IeC {\'\i }a}{35}{section.3.1}}
\newlabel{cap3:sec:datosSST}{{3.1}{35}{Datos de \tsm {} y metodología\relax }{section.3.1}{}}
\citation{Kaufman1990}
\citation{R2010}
\@writefile{toc}{\contentsline {section}{\numberline {3.2}An\'alisis de la temperatura superficial del mar}{36}{section.3.2}}
\newlabel{cap3:sec:analisisSST}{{3.2}{36}{Análisis de la \tsm \relax }{section.3.2}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Media mensual de la temperatura superficial del mar{}}}{37}{figure.caption.8}}
\newlabel{fig:globalSSTmean}{{3.1}{37}{Media mensual de la \tsm {}\relax }{figure.caption.8}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2.1}Climatolog\IeC {\'\i }a}{38}{subsection.3.2.1}}
\newlabel{cap3:sec:temporalSST}{{3.2.1}{38}{Climatología\relax }{subsection.3.2.1}{}}
\citation{R2010}
\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Ciclo anual de la temperatura superficial del mar{}}}{39}{figure.caption.9}}
\newlabel{fig:annualSST}{{3.2}{39}{Ciclo anual de la \tsm {}\relax }{figure.caption.9}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {3.3}{\ignorespaces Temperatura superficial del mar media mensual Agosto 2003}}{39}{figure.caption.10}}
\newlabel{fig:SST200308}{{3.3}{39}{Temperatura superficial del mar media mensual Agosto 2003\relax }{figure.caption.10}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces Anomal\IeC {\'\i }a de temperatura superficial del mar media mensual Agosto 2003}}{40}{figure.caption.11}}
\newlabel{fig:SSTanom200308}{{3.4}{40}{Anomalía de temperatura superficial del mar media mensual Agosto 2003\relax }{figure.caption.11}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2.2}Distribuci\'on espacial}{40}{subsection.3.2.2}}
\newlabel{cap3:sec:espacialSST}{{3.2.2}{40}{Distribución espacial\relax }{subsection.3.2.2}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces Temperatura superficial del mar media mensual y cl\'ustering verano-invierno}}{41}{figure.caption.12}}
\newlabel{fig:SSTclustering}{{3.5}{41}{Temperatura superficial del mar media mensual y clústering verano-invierno\relax }{figure.caption.12}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2.3}Conclusi\'on - Resumen}{42}{subsection.3.2.3}}
\@writefile{lot}{\contentsline {table}{\numberline {3.1}{\ignorespaces TSM media}}{44}{table.caption.13}}
\newlabel{cap3:tab:tsmmedia}{{3.1}{44}{TSM media\relax }{table.caption.13}{}}
\@setckpt{Capitulos/03ClimatologiaSST}{
\setcounter{page}{45}
\setcounter{equation}{1}
\setcounter{enumi}{4}
\setcounter{enumii}{0}
\setcounter{enumiii}{0}
\setcounter{enumiv}{0}
\setcounter{footnote}{1}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{3}
\setcounter{section}{2}
\setcounter{subsection}{3}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
\setcounter{figure}{5}
\setcounter{table}{1}
\setcounter{parentequation}{0}
\setcounter{LT@tables}{0}
\setcounter{LT@chunks}{0}
\setcounter{float@type}{8}
\setcounter{NAT@ctr}{0}
\setcounter{Item}{9}
\setcounter{Hfootnote}{1}
\setcounter{bookmark@seq@number}{29}
\setcounter{ContinuedFloat}{0}
\setcounter{KVtest}{0}
\setcounter{subfigure}{0}
\setcounter{subfigure@save}{2}
\setcounter{lofdepth}{1}
\setcounter{subtable}{0}
\setcounter{subtable@save}{0}
\setcounter{lotdepth}{1}
\setcounter{lstnumber}{1}
\setcounter{section@level}{0}
\setcounter{lstlisting}{0}
}

.auxfiles for anything which could produce an 'F'. These files are read in after the last page have been flushed and can add new material, which then would appear on an extra page. The same is true for\AtEndDocument{..}. – Martin Scharrer♦ Apr 4 '12 at 12:00\includecommand, but by the\chapterinside it. So, if the fileCapitulos/04Modelizacion.texcontains anything (say, anF) before the\chapter, this will cause exactly the effect you're seeing. – Stephan Lehmke Apr 14 '12 at 20:44