I will tell you what I know, hopefully its right! heheh
Pretty much FF used some sort of advanced tool to calculate your coverline and timing and all sorta stuff like that... Your coverline comes after you have a significant rise in temp, over 3 days. It also looks at the other data that you put in (CM and OPK and CP)..
As for the AF coming and the temp not dropping below the coverline.. not sure! Their temp was probably right, but maybe their coverline will change next cycle. Everyone is different but an 'ideal' chart, your temp would stay above the cover line and if there is a pregnancy then the temp should keep rising in an ideal chart.
Hopefully my answer is alright, but I am sure one of the chart gurus in jump in and correct me! I just finished my FF course this week so I am still learning.
Have you done the FF course? Its really informative and I have learnt alot!
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