Let me reassure you that at 16 months, he is definitely waking out of habit for that midnight bottle. What you do when he wakes for it will make all of the difference. It sounds to me that your son might not have the skills to put himself back to sleep at night (and naps, since you mentioned he only naps for 25 minutes max) when he wakes. Does he put himself to sleep or do you use something to get him to sleep? Is he on EASY? Have you read any of the Baby Whisperer books? Sorry for all the questions, but they will help get you on the right track with your son's night wakings!
Let me know, and we'll try to get you some answers