Automation testing with Selenium PHP faces challenges due to dynamically loaded web elements through AJAX and JavaScript, which can lead to synchronization issues. Selenium WebDriver does not track the real-time state of the Document Object Model (DOM), making it susceptible to exceptions like 'element not clickable'. To address these issues, Selenium offers implicit and explicit wait commands to synchronize timing in web automation. Implicit wait sets a global delay for the WebDriver to poll the DOM, while explicit wait halts execution until a specific condition is met. Explicit wait is more versatile, allowing for conditions such as visibility or clickability of elements, and is preferred for managing synchronization between the browser and the Selenium script. Implicit wait is simpler but less reliable, as it applies globally and may not handle complex scenarios efficiently. Overall, synchronization in Selenium is crucial for robust test automation, and explicit wait is recommended over implicit wait due to its precision and flexibility.