It looks like you are using a background image for the first page of your chapter. This option works best with a full-page image. In an ePub, the image will be cropped automatically to stay in the header, but in a PDF, it will extend down the page and appear behind both the header and body text if it's tall enough.
If you're using a smaller image, the best approach is to use the image element instead. This keeps the image positioned in the header without interfering with the body text.
If you'd rather stick with a background image, you may need to crop it so it only appears above the body text. To do this, keep the width the same and adjust only the height.