problematic is your second table. it is wider than column width. it is posible to make narrower, however content of table is unknown, so the obtained result probably in real document twill not work.

[![enter image description here][1]][1]

as you can see, i change table layout. to my taste has now better look-out. for this i add two new packages: `booktabs` for rules and `siunitx` for `S` column type. i also assume that content of column header is the widest cells contents.

 \documentclass[10pt,twocolumn,letterpaper]{article}
 \usepackage{siunitx}
 \usepackage{array, booktabs}
 \newcommand\mc[1]{\multicolumn{1}{>{\bfseries}c}{#1}}

 \usepackage{lipsum}

 \begin{document}
 \section{Results}
 \label{Sec:results}
 \lipsum[22]
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Table
 \begin{table}[htb]
 \centering
 \begin{tabular}{l l S[table-format=2.1]}
 \toprule
 \mc{Method} & \mc{Input} & \mc{Accuracy} \\
 \midrule
 3DShapeNets & volumetric & 84.7 \\
 Voxnet & volumetric & 85.9 \\
 \midrule
 PointNet & points & 89.2 \\
 PointNet++ & points & 90.7 \\
 Kd-network & points & {91.8 / 90.6} \\
 \midrule
 Ours & points & {?} \\
 \bottomrule
 \end{tabular}
 \caption{Classification Accuracy on ModelNet40 dataset}
 \label{table:ClassificationAcc}
 \end{table}
 \lipsum[44]
 \begin{table}[htb]
 \centering
 \begin{tabular}{ l l l l}
 \toprule
 \mc{Method} & \mc{Data} & \mc{Permutations} & \mc{Points} \\
 \midrule
 PointNet & & & \\
 PointNet++ & & & \\
 Kd-Network & & & \\
 \bottomrule
 \end{tabular}
 \caption{Challenges summary }
 \label{table:ChallangeComp}
 \end{table}
 \lipsum

 \subsection{Architecture Design Analysis}
 \label{SubSec:Arch_Dn_Analysis}

 \subsection{Visualizations}
 \label{SubSec:Vis}
 \end{document}

above *mwe* gives no error, no warning, no bad boxes.

 [1]: https://i.sstatic.net/fobTS.png