If I use SmallCapsFeatures={Renderer=Basic} as an option when setting the main font of the document, I get an obviously wrong ligature in the small caps shape. In the MWE the letters T and h are not typeset as separate glyphs in small caps but as a Th-ligature in regular upright shape. This is the case also with other ligature combinations, such as fl.
MWE:
\documentclass{article}
\usepackage{fontspec}
\setmainfont[SmallCapsFeatures={Renderer=Basic}]{Linux Libertine O}
\begin{document}
\textsc{Thomson} \textsc{T\/homson}
\end{document}
Removing SmallCapsFeatures={Renderer=Basic} makes the problem go away. But I need this option in order to make use of the tracking feature of the microtype package.
How to circumvent this behaviour? Am I doing something wrong?
EDIT: Using the following makes the mentioned problem go away:
\setmainfont[SmallCapsFeatures={Renderer=Basic,Ligatures={NoCommon}}]{Linux Libertine O}
However, I wonder what I might be missing by this workaround...

microtypedocumentation,Renderer=Basicis no longer required. – Thérèse Jul 15 '16 at 19:31