There's a strong relationship between the degree of fullness of the breast and the fat content of the milk. When your breasts are full, there is less fat content. When they are well drained, there is more fat content. The fat content increases gradually over the course of a feeding. However ALL of the components of breastmilk are essential for the growth of your baby, not just its fat content.
If you've ever been told your milk is "low fat," you were most likely made to unnecessarily worry by someone who doesn't understand how milk production works and how dynamic breastmilk is. All that matters is that your baby is thriving.
The fatty layer in your pumped milk is never a good determinant of whether you have "low fat" milk or not. Remember that one pump session is just a snapshot in time and doesn't provide an accurate picture of your total fat yield in a 24 hour day.
From Kellymom: The research tells us that baby's milk intake (the volume of milk -- not the amount of fat in that milk) is the only thing that has been correlated with infant growth in exclusively breastfed babies.