Latex: TeXMaker does not compile - several unsolved errors - compilation

Question

I am working on a protocol using TeXMaker. I switched from Eclipse+Texlipse to Texmaker and what compiled successfully before, does not compile anymore.
I have a main.tex file, which contains the structure of my protocol. I have several tex-files as inputs and a design.sty, which provides my design. I want to compile and create the PDF-protocol.
When I try to execute the following code in TeXMaker (the main.tex):
\documentclass[11pt,a4paper,oneside,listof=totoc, bibliography=totoc
version=first]{scrreprt}
\usepackage{design}
\begin{document}
\pagenumbering{arabic}
% cover
\input{./cover.tex}
% introduction
\newpage
\chapter{Introduction}
\section{Synmikro}
\input{./synmicro.tex}
\section{Genetic Switches}
\input{./switches.tex}
\section{ECFs}
\input{./ECF.tex}
\section{Sinorhizobium Meliloti}
\input{./meliloti.tex}
\newpage
\section{Laboratory Internship}
\input{./internship.tex}
\section{Bioinformatics}
\input{./bioinfo.tex}
% materials and methods
\newpage
\chapter{Material and Methods}
\section{Used strains}
\input{./MMexoECFs.tex}
\section{Cultivation conditions}
\input{./MMcultivation.tex}
\section{RNA preparation}
\input{./MMrNAprep.tex}
\section{Quality control of total RNA}
\input{./MMtotalRNAQC.tex}
%\section{Quality control}
% \subsection{PCR and Agarose gel}
% \input{./MMnormPCR.tex}
%\subsection{RNA purity and integrity control}
% \input{./MMbioanalyzer.tex}
\section{qRT-PCR}
\input{./MMqRTPCR.tex}
%\section{QBit}
% \input{./MMqbit.tex}
\section{Bioinformatics}
\input{./MMbioinfo.tex}
\subsection{Non-restrictive approach}
\input{./MMnonRestrictive.tex}
\subsection{Levenshtein distance}
\input{./MMlev2.tex}
\subsection{Feature Search}
\input{./MMfeatureSearch.tex}
%\subsection{Position Specific Scoring Matrices}
% \input{./MMpssm.tex}
% results
\newpage
\chapter{Results}
%\section{Agarose Gel}
% \input{./Ragarose.tex}
\section{Nanodrop and Bioanalyzer}
\input{./Rbioanalyzer.tex}
%\section{Qbit}
% \input{./Rqubit.tex}
\newpage
\section{Real-Time PCR}
\input{./RRTpCR.tex}
\newpage
\section{Bioinformatics}
\input{./Rbioinfo.tex}
% discussion
\end{document}
TeXMaker gives me several errors for main.tex. They are:
Line 47: File ended while scanning use of \caption#xdblarg
Line 79: !Latex Error: \begin{figure} on input line 7 ended by \end{document}
Line 79: !You can't use '\end’ in internal vertical mode
Line 79: !Latex Error: \begin{figure} on input line 7 ended by \end{document}
! Missing } inserted
Line 1: ! Emergency stop. <*> main.tex ***(job aborted, no legal \end found)
Line 47 is "\input{./MMqRTPCR.tex}
Line 79 is "\end{document}"
I am honestly confused. TeXMaker's error description is about missing braces. Am I screen-blind? I checked the braces 3 times and cannot figure out, what I missed. So, I am guessing, I missed something crucial about Latex.
Thanks for any help!
UPDATE:
In the input file "MMqRTPCR.tex", I out-commented a figure and all errors are gone. Here is the content of the file.
TEXTEXTEXT
%\begin{figure}[H]
%\centering
% \includegraphics[scale=0.6,natwidth=764,natheight=218]%{deltaDeltaCorrectedFormula.png}
% \caption{mycaption}
%\label{deltaDelta}
%\end{figure}
TEXTEXTEXT
\begin{table}[!h]
\centering
\caption{Primer sequences and targets}
\label{table1}
\begin{tabular}{|l|l|l|ll}
\cline{1-3}
Primer Sequence & Target & Direction \\ \cline{1-3}
AACATGTGCCGGTTGATAG & ECF20_992 & forward \\ \cline{1-3}
GCTGCTTCGGTATTGCTCA & ECF20_992 & reverse \\ \cline{1-3}
TCGTACCATTGAAAGCCTG & ECF02_2817 & forward \\ \cline{1-3}
ATCAATGGCTTCACGTGCA & ECF02_2817 & reverse \\ \cline{1-3}
TTCAAGAAACCATGGCCAC & ECF11_987 & forward \\ \cline{1-3}
GCTCGGCCAAATATCATCG & ECF11_987 & reverse \\ \cline{1-3}
\end{tabular}
\end{table}
TEXTEXTEXT
** UPDATE & SOLUTION**
The error was not in the main.tex itself, but in an input file. So, when TeXMaker tells you about missing bracers, jump to the line, where the error occured in the main.tex and check the bracers in the input file, which you see there.

Answer 1

So,
the error was a missing curly brace after all! Yet, it was not missing in the main.tex, but in the input file within the figure caption!
Thanks anybody, who's brain might have melted trying to find a solution to my problem. I hope this helps others, if they encounter the same error. :)