The MWE reproducing the problem can be reduced to:
\documentclass{scrreprt}
\usepackage{classicthesis}
\begin{document}
\begin{table}
\caption{test}
\end{table}
\appendix
\chapter{Appendix} Hello
\end{document}
which produces the undesired behaviour shown here:

The problem occurs in my TeX Live2011 system; here's the File List obtained adding \listfiles to my MWE:
*File List*
scrreprt.cls 2011/06/16 v3.09a KOMA-Script document class (report)
scrkbase.sty 2011/06/16 v3.09a KOMA-Script package (KOMA-Script-dependent ba
sics and keyval usage)
scrbase.sty 2011/06/16 v3.09a KOMA-Script package (KOMA-Script-independent
basics and keyval usage)
keyval.sty 1999/03/16 v1.13 key=value parser (DPC)
scrlfile.sty 2011/03/09 v3.09 KOMA-Script package (loading files)
tocbasic.sty 2011/05/30 v3.09a KOMA-Script package (handling toc-files)
scrsize11pt.clo 2011/06/16 v3.09a KOMA-Script font size class option (11pt)
typearea.sty 2011/06/16 v3.09a KOMA-Script package (type area)
classicthesis.sty 2011/06/05 v3.0 Typographic Style for a classic-looking th
esis
ifthen.sty 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
ifpdf.sty 2011/01/30 v2.3 Provides the ifpdf switch (HO)
hyperref.sty 2011/08/19 v6.82h Hypertext links for LaTeX
hobsub-hyperref.sty 2011/04/23 v1.4 Bundle oberdiek, subset hyperref (HO)
hobsub-generic.sty 2011/04/23 v1.4 Bundle oberdiek, subset generic (HO)
hobsub.sty 2011/04/23 v1.4 Subsetting bundle oberdiek (HO)
infwarerr.sty 2010/04/08 v1.3 Providing info/warning/message (HO)
ltxcmds.sty 2011/04/18 v1.20 LaTeX kernel commands for general use (HO)
ifluatex.sty 2010/03/01 v1.3 Provides the ifluatex switch (HO)
ifvtex.sty 2010/03/01 v1.5 Switches for detecting VTeX and its modes (HO)
intcalc.sty 2007/09/27 v1.1 Expandable integer calculations (HO)
etexcmds.sty 2011/02/16 v1.5 Prefix for e-TeX command names (HO)
kvsetkeys.sty 2011/04/07 v1.13 Key value parser (HO)
kvdefinekeys.sty 2011/04/07 v1.3 Defining keys (HO)
pdftexcmds.sty 2011/04/22 v0.16 Utilities of pdfTeX for LuaTeX (HO)
pdfescape.sty 2011/04/04 v1.12 Provides string conversions (HO)
bigintcalc.sty 2011/01/30 v1.2 Expandable big integer calculations (HO)
bitset.sty 2011/01/30 v1.1 Data type bit set (HO)
uniquecounter.sty 2011/01/30 v1.2 Provides unlimited unique counter (HO)
letltxmacro.sty 2010/09/02 v1.4 Let assignment for LaTeX macros (HO)
hopatch.sty 2011/01/30 v1.0 Wrapper for package hooks (HO)
xcolor-patch.sty 2011/01/30 xcolor patch
atveryend.sty 2011/04/23 v1.7 Hooks at very end of document (HO)
atbegshi.sty 2011/01/30 v1.15 At begin shipout hook (HO)
refcount.sty 2010/12/01 v3.2 Data extraction from references (HO)
hycolor.sty 2011/01/30 v1.7 Color options of hyperref/bookmark (HO)
ifxetex.sty 2010/09/12 v0.6 Provides ifxetex conditional
kvoptions.sty 2010/12/23 v3.10 Keyval support for LaTeX options (HO)
pd1enc.def 2011/08/19 v6.82h Hyperref: PDFDocEncoding definition (HO)
hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
url.sty 2006/04/12 ver 3.3 Verb mode for urls, etc.
hpdftex.def 2011/08/19 v6.82h Hyperref driver for pdfTeX
rerunfilecheck.sty 2011/04/15 v1.7 Rerun checks for auxiliary files (HO)
xcolor.sty 2007/01/21 v2.11 LaTeX color extensions (UK)
color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
dvipsnam.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
mathpazo.sty 2005/04/12 PSNFSS-v9.2a Palatino w/ Pazo Math (D.Puga, WaS)
microtype.sty 2010/01/10 v2.4 Micro-typography with pdfTeX (RS)
microtype.cfg 2010/01/10 v2.4 microtype main configuration file (RS)
booktabs.sty 2005/04/14 v1.61803 publication quality tables
textcase.sty 2004/10/07 v0.07 Text only upper/lower case changing (DPC)
soul.sty 2003/11/17 v2.4 letterspacing/underlining (mf)
scrpage2.sty 2010/04/22 v2.5 LaTeX2e KOMA-Script package
titlesec.sty 2011/08/28 v2.9.1 Sectioning titles
tocloft.sty 2010/10/13 v2.3e parameterised ToC, etc., typesetting
scrtime.sty 2011/06/16 v3.09a KOMA-Script package (time of LaTeX run)
remreset.sty
ot1pplj.fd 2004/09/06 font definitions for OT1/pplj.
nameref.sty 2010/04/30 v2.40 Cross-referencing by name of section
gettitlestring.sty 2010/12/03 v1.4 Cleanup title references (HO)
a.out
a.out
supp-pdf.mkii
mt-ppl.cfg 2005/11/16 v1.6 microtype config. file: Palatino (RS)
***********
The problem can be solved in two ways:
1) Using the numbers=noenddot option for the KOMA classes (this will suppress the spurious extra period from the MWE) and then changing the label separator for the captions using \captionsetup from the caption package:
\documentclass[numbers=noenddot]{scrreprt}
\usepackage{classicthesis}
\usepackage{caption}
\captionsetup{labelsep=period}
\begin{document}
\begin{table}
\caption{test}
\end{table}
\appendix
\chapter{Appendix} Hello
\end{document}
2) Redefining \tableformat (and \figureformat) to suppress the \autodot inserted by default (again, the label separator for the captions was changed using \captionsetup from the caption package):
\documentclass{scrreprt}
\usepackage{classicthesis}
\usepackage{caption}
\captionsetup{labelsep=period}
\renewcommand*{\figureformat}{\figurename~\thefigure}
\renewcommand*{\tableformat}{\tablename~\thetable}
\begin{document}
\begin{table}
\caption{test}
\end{table}
\appendix
\chapter{Appendix} Hello
\end{document}