As much science as there is behind fertility charting I think that there is a lot of art behind it as well. What is true for one body may not be true for another. That being said, typically when I wake up in the middle of the night and I take my temp in the morning it does appear off (sometimes warmer sometimes colder). On those days I mark it in FF as "sleep deprived" and it will mark it with an open circle. Then later in my cycle I will either discard that temp or just take it with a grain of salt so to speak.
Sorry I don't have a more scientific answer for you. Hopefully some of the girls here with more experience will chime in.