Java – What are the most common programming mistakes PHP programmers make in Java

Popularity ≠ Quality. Most people using a shopping cart won't be testing it properly. Of course, that's true for all languages. I advise that you audit all proposed cart solutions for security, paying particular attention to SQL Injection and XSS issues. (This is important because you've got code that's going to be fairly close to handling money, so it will be more exposed than most of your site in any case.)

As for advantages of PHP over Java or vice versa, it really depends what you've done your web tier in. There's a big advantage in any case with keeping the number of languages in use within any particular tier down, as it lets developers specialize across the whole tier. (It's nice to be able to do anything, but there's only 24 hours per day for Earth-bound folks.) Fitting in with what you're doing currently is more important than chasing whatever is “hot”, particularly for core competencies (like selling your products).