I got this; "If you have to get up in the night and it is unavoidable, like having to take care of a small child, or if you have to go to the bathroom, just do the best you can. Take your temperature as close as you can to the same time each morning and choose a time that is likely to be when you have had the most sleep. For example, if your toddler wakes up every morning at 6 am, then take your temperature at that time, even if you go back to sleep. Try to avoid taking your temperature in the middle of the night, though, even if you seem to always get up at the same time in the middle of the night. Temperatures taken in the morning show a clearer biphasic curve and the time is more predictable."
from here;
https://sites.google.com/site/gpnest...add-l-bbt-tips
That being said, I know my son wakes up anywhere from 4-6 AM so I set my alarm and temp at 4. My temps have been a bit jumpy too, but I am still able to see when I ovulated. (it was CD21, just waiting for FF to confirm)