Graphics and Proofs

Using a YalePhD theses class with various tweaks I have:
Problem 1) Proof symbol prints before the end of the proof
Problem 2) Graphics/Figures with different references produce the same Figure number in the caption as each other
NOTES: Here comes Preamble and Packages - (many lines)
\theoremstyle{change}
\theoremheaderfont{\normalfont\bfseries}
\geometry{left=1in,right=1in,top=1in,bottom=1in}
\iffalse
\newenvironment{proof}[1][Proof]{\normalfont\noindent\textbf{#1.} }{\ \rule{0.5em}{0.5em}}
\fi
\newtheorem{theorem}{Theorem}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
{\theorembodyfont{\upshape}
\newtheorem{acknowledgement}[theorem]{Acknowledgement}
\newtheorem{algorithm}[theorem]{Algorithm}
\newtheorem{axiom}[theorem]{Axiom}
\newtheorem{case}[theorem]{Case}
\newtheorem{claim}[theorem]{Claim}
\newtheorem{conclusion}[theorem]{Conclusion}
\newtheorem{condition}[theorem]{Condition}
\newtheorem{conjecture}[theorem]{Conjecture}
\newtheorem{criterion}[theorem]{Criterion}
\newtheorem{definition}[theorem]{Definition}
\newtheorem{example}[theorem]{Example}
\newtheorem{exercise}[theorem]{Exercise}
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{problem}[theorem]{Problem}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{solution}[theorem]{Solution}
\newtheorem{summary}[theorem]{Summary}
}
____________
PACKAGES AND EARLY LINES OF CLASS

%\geometry{left=1in,right=1in,top=1in,bottom=1in}
%READING SPACER - PBos
%\titlespacing{\chapter}{0pt}{0pt}{1cm}

\documentclass[11pt]{yalephd}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage[a4paper]{geometry}
\usepackage{graphicx}
\usepackage[amsmath,amsthm,hyperref,thmmarks]{ntheorem}
\usepackage{ulem}
\usepackage{setspace}
\usepackage{tocbibind}
\usepackage[Lenny]{fncychap}
\usepackage[compact]{titlesec}
\usepackage[a4paper, linktocpage]{hyperref}

\setcounter{MaxMatrixCols}{10}
%TCIDATA{OutputFilter=LATEX.DLL}
%TCIDATA{Version=5.50.0.2960}
%TCIDATA{}
%TCIDATA{BibliographyScheme=Manual}
%TCIDATA{Created=Sunday, November 11, 2018 21:04:21}
%TCIDATA{LastRevised=Sunday, December 02, 2018 12:00:35}
%TCIDATA{}
%TCIDATA{}
%TCIDATA{Language=American English}
%TCIDATA{CSTFile=yalephd.cst}

\theoremstyle{change}
\theoremheaderfont{\normalfont\bfseries}
\geometry{left=1in,right=1in,top=1in,bottom=1in}
\iffalse
\newenvironment{proof}[1][Proof]{\normalfont\noindent\textbf{#1.} }{\ \rule{0.5em}{0.5em}}
\fi
\newtheorem{theorem}{Theorem}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
{\theorembodyfont{\upshape}
\newtheorem{acknowledgement}[theorem]{Acknowledgement}
\newtheorem{algorithm}[theorem]{Algorithm}
\newtheorem{axiom}[theorem]{Axiom}
\newtheorem{case}[theorem]{Case}
\newtheorem{claim}[theorem]{Claim}
\newtheorem{conclusion}[theorem]{Conclusion}
\newtheorem{condition}[theorem]{Condition}
\newtheorem{conjecture}[theorem]{Conjecture}
\newtheorem{criterion}[theorem]{Criterion}
\newtheorem{definition}[theorem]{Definition}
\newtheorem{example}[theorem]{Example}
\newtheorem{exercise}[theorem]{Exercise}
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{problem}[theorem]{Problem}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{solution}[theorem]{Solution}
\newtheorem{summary}[theorem]{Summary}
}
\renewcommand\proofSymbol{\ensuremath{\raisebox{0.0em}{\rule{0.5em}{0.5em}}}}
\input{tcilatex}
\begin{document}

\frontmatter
\title{Improving Dirichlet's Theorem:\\
Lebesgue and Hausdorff Measure Theory.}
\author{Philip Bos}
\date{November 2018}
\advisor{Mumtaz Hussain}
\maketitle

\begin{abstract}
Something new and important.\pagebreak
\end{abstract}

\tableofcontents

\chapter*{Preface}

John MacKendrick's picture

I am not able to reproduce

I am not able to reproduce either problem. 

Make sure that the entire body of the proof is actually in the proof environment. Pressing <Enter> will create a new paragraph for the proof, but pressing <F2> will end the proof. 

When you are entering figures, make sure that the placement is set to Floating in order for the numbering to be applied appropriately.

Please feel free to post a minimum working example of your problems or to send them to support@mackichan.com.