Technically, Pilates is a specific series of exercises that one should follow in a particular order. BUT I think it's fun to mix it up, add in some different elements that are still true to Pilates and keep it fresh and fun.
Pilates is supposed to be a full body workout every time. It's also supposed to be a 55 minute workout. When you are short on time that doesn't mean you have to give up your practice. When you want to focus on a particular area, I say go for it!