Once the recommendation came to limit milk I have always given milk in addition to a meal (after they have eaten). With my own kids I just give them one cup before nap (after they've eaten a healthy lunch) and after bath, before bed. My girls love milk and would drink a bag a day if I let them.

My cousin was giving their boy a big bottle upon waking up (18 mos at the time) before breakfast and they wondered why he never eats and is small for his age. They had gotten into the pattern when he was on formula and couldn't understand the concept of having milk after a meal or in between a meal. Like Playfelt said, sometimes they just get into a pattern or doing things "just cause" without much thought.