When saving figures as PDFs in MATLAB, issues arise with landscape images being cut off to fit a portrait page. The default behavior of MATLAB's PDF export is linked to the window size of the figure, which can lead to poor quality outputs, such as jagged edges. To improve the situation, users are advised to create a startup script that sets the default paper type to A4 and adjusts the paper units and position mode. This ensures that figures are appropriately scaled for better presentation. Additionally, saving figures as EPS before converting to PDF is recommended for higher quality results.