I know this is a biglong shot since I cannot really post a minimal working example, but I'll try to describe the issue to the best of my capabilities. I'm running pdflatex twice for the compilation.

I have the following testing macro, which produces the expected result at the beginning of the chapter.

\def\myTest{
Text1. \marginnote[left]{right}

Some more text. \marginnote[left]{right}

More text, longer sentence. \marginnote[left]{right}}

Unfortunately, after a few pages, marginnote gets confused.

It looks like the first call to \marginnote[left]{right} fixes the alignment for the following two instances.

One could simply use marginpar. I noticed this issue when trying to use sidecaption, which was putting the text over the figure rather than in the margin.

Original issue

\begin{figure}[H]
  \centering
  \sidecaption{Something.}
  \sidecaption{Something.}
  \caption{Disappeared.}
  \input{inference-figs/activation}
\end{figure}