Which PS Version do you have? Are you using an URL Cleaner? I have the same issue as you, and I found out why. I am using the SEO Performance (URL cleaner) and Google sitemap. I have used it for a long time and it always worked fine until about 2 months ago. Anways... when I manually generate a sitemap, it renders it with the correct URLs (the cleaned ones). When generated through the Cron job, which has been my default way of doing it, it does not use the cleaned URLs but uses Prestashop default, including id numbers. The Problem now for me is that I submitted an URL to google through the sitemap, which is not reflected on my website, causing Google to exclude it.
Example: So the URL of a product is www.example.com/product-1 (cleaned with URL Cleaner). The sitemap generates the URL as www.example.com/1-category/123-product-1.