I recently experienced several issues after some packages got updated. The one remaining is that hyperref doesn't recognize \subsubsection{} anymore when using the apa6 class. The bookmarks in the PDF output are displayed as <Untitled>. The same is true for the example provided in the apa6 documentation. I added a minimal example that also produces the erroneous bookmarks. All the other referencing (citations, etc.) seems to work just fine.
\documentclass[jou]{apa6}
\usepackage{hyperref}
\usepackage[american]{babel}
\usepackage{csquotes}
\usepackage[style=apa,sortcites=true,sorting=nyt]{biblatex}
\DeclareLanguageMapping{american}{american-apa}
\addbibresource{bibliography.bib}
\title{Sample}
\author{Author}
\affiliation{University}
\leftheader{Author}
\abstract{This is a test abstract.}
\keywords{APA6}
\begin{document}
\maketitle
\section{Method}
\subsection{Materials}
Several materials were used for this project. Some of them were
\subsubsection{Paper-and-Pencil Instrument}
We used an instrument that we found to be highly successful.
\printbibliography
\end{document}
