In principle, php is indistinguishable from standard HTML to the search engines because all they see is the HTML that your PHP code produces. So the issue is not the use of PHP, but the content of these pages. Dynamic pages are subject to cookie-cutter-itis where the <title>s and <meta> information content is duplicated on many pages. This can be seen as a signal of poor quality to Google. A heavy ratio of template content to unique content among these pages can also be a problem. It's a fuzzy area and I'm sure others will have more suggestions.