What's the time gap between 03:05 and 03:06? Apollo has lost a lot of weight.
What is the nature of the disease? Is it a coincidence that the humanoid cylons are susceptible to the same kinds of diseases that the centurions, the raiders, and the hybrids are?
Why are the cylons worried about the possibility of a disease that can be carried with dying cylons through the downloading process?
Why didn't the hybrid want to leave the stricken base ship?
Why don't hybrids get votes?
Of course I'm on record for quite some time as claiming Gaius Baltar Is A Cylon. This episode was a little heavy-handed in bringing the question out to the viewers.
Six claims that the current seven models do not talk about the other five models. This could be due to some schism. It could also be due to some sort of active division between the cylons, which would explain why the cylons occupying New Caprica were concerned about protecting the resurrection ship. Depending on the nature of the schism, it is not impossible that these instances of the seven cylon models we know are unaware of the physical characteristics of the remaining five, so that they would not recognize an instance of the remaining five if they met one. Such a division would also represent the obvious third party (the one I labeled as god) hinted at late last season.