In addition to followfollowing David Carlisle's sage advice to add the [t] positioning specifier to both tabularx environments, you may also want to (a) use the macros of a package such as mhchem to simplify and streamline the typesetting of chemical formulas and (b) use the booktabs package and its \toprule, \midrule, \bottomrule, and \addlinespace macros (and stop using \hline...) to give the tables a more and inviting "look".
In addition to follow David Carlisle's sage advice to add the [t] positioning specifier to both tabularx environments, you may also want to (a) use the macros of a package such as mhchem to simplify and streamline the typesetting of chemical formulas and (b) use the booktabs package and its \toprule, \midrule, \bottomrule, and \addlinespace macros to give the tables a more and inviting "look".
\documentclass{article} % or some other suitable document class
\usepackage{iftex} \ifpdftex\usepackage[T1]{fontenc}\fi
\usepackage{tabularx,upgreek,mhchem,booktabs}
\hyphenation{iso-prene di-terpene tri-terpene mono-terpene
sesqui-terpene}
\begin{document}
\begin{table}[t]
\caption{List of compounds in mixed stock solution. }
\smallskip
iso: isoprene, mt: monoterpene, omt: oxygenated monoterpene, sqt: sesquiterpene, osqt: oxygenated sesquiterpene, dt: diterpene, tt: triterpene.
\smallskip
\begin{tabularx}{0.48\textwidth}[t]{@{} Xll @{}}
\toprule
Compound & Type & Formula \\
\midrule
Isoprene & iso & \ce{C5H8} \\
$\upalpha$-Pinene & mt & \ce{C10H16} \\
Camphene & mt & \ce{C10H16} \\
Sabinene & mt & \ce{C10H16} \\
$\upbeta$-Pinene & mt & \ce{C10H16} \\ \addlinespace
$\upbeta$-Myrcene & mt & \ce{C10H16} \\
$\upalpha$-Phellandrene & mt & \ce{C10H16} \\
3-Carene & mt & \ce{C10H16} \\
$\upalpha$-Terpinene & mt & \ce{C10H16} \\
\textit{m}-Cymene & mt & \ce{C10H14} \\ \addlinespace
\textit{p}-Cymene & mt & \ce{C10H14} \\
Ocimene & mt & \ce{C10H16} \\
Eucalyptol & omt & \ce{C10H18O} \\
\textit{D}-Limonene & mt & \ce{C10H16} \\
\textit{o}-Cymene & mt & \ce{C10H14} \\ \addlinespace
$\upgamma$-Terpinene & mt & \ce{C10H16} \\
Sabinene Hydrate & omt & \ce{C10H18O} \\
Terpinolene & mt & \ce{C10H16} \\
Linalool & omt & \ce{C10H18O} \\
Fenchol & omt & \ce{C10H18O} \\ \addlinespace
Isopulegol & omt & \ce{C10H18O} \\
\\ % optional: blank line
\bottomrule
\end{tabularx}\hspace{\fill} % maximize horizontal separation
\begin{tabularx}{0.48\textwidth}[t]{@{} Xll @{}}
\toprule
Compound & Type & Formula \\
\midrule
Isoborneol & omt & \ce{C10H18O} \\
($-$)-Borneol & omt & \ce{C10H18O} \\
($+$)-Borneol & omt & \ce{C10H18O} \\
Menthol & omt & \ce{C10H20O} \\
Terpinen-4-ol & omt & \ce{C10H18O} \\ \addlinespace
$\upalpha$-Terpineol & omt & \ce{C10H18O} \\
Citronellol & omt & \ce{C10H20O} \\
Carvacrol & omt & \ce{C10H14O} \\
Geraniol & omt & \ce{C10H18O} \\
Thymol & omt & \ce{C10H14O} \\ \addlinespace
($-$)-$\upalpha$-Cedrene & sqt & \ce{C15H24} \\
Caryophyllene & sqt & \ce{C15H24} \\
trans-$\upbeta$-Farnesene & sqt & \ce{C15H24} \\
Humulene & sqt & \ce{C15H24} \\
Valencene & sqt & \ce{C15H24} \\ \addlinespace
Nerolidol & osqt & \ce{C15H26O} \\
Guaiol & osqt & \ce{C15H26O} \\
Cedrol & osqt & \ce{C15H26O} \\
($-$)-$\upalpha$-Bisabolol & osqt & \ce{C15H26O} \\
Farnesol & osqt & \ce{C15H26O} \\ \addlinespace
Phytane & dt & \ce{C20H42} \\
Squalene & tt & \ce{C30H50} \\
\bottomrule
\end{tabularx}
\end{table}
\end{document}