I had this happen also, I wiped out all but the homeworld of a AI. Planets 2-3-4 jumps away still had the culture lines for a long long time and if I tryied takeing them over they reverted imedietly to AI.
the AI's enpire was totaled, it has no more brodcasters and even planets far away from the AI's last planet where still impervious to all colonization. even though all 'life' had been wiped out for all of those planets for quite some time.
Then a planet close to the homeworld allowed me to take it over?!? but still not the others farther way . . . then a AI team mate got them right from under me.
kind of strange, possably a decay bug? it should decay quite quickly if everything in a few jumps are sterilized.