Yamata no Orochi had been heavily wounded by Susanoo in their first fight. Not only had Susanoo taken away Kusanagi, but also the Core of Yamata no Orochi. It was the reason Basil dared to risk his life on fighting it.
Unlike any other low class Beasts, higher class Beasts wouldn't die if their core was taken. Therefore, to kill a higher class Beast one needed to do it meticulously. One miss would let the Beast one had defeated escape.
Basil guessed it might be the case with Susanoo. Even though people called him a God, he believed that Susanoo was no different than any other human. Therefore, he made a mistake. He must have thought Yamata no Orochi had been dead.
No one knew that Yamata no Orochi had had its Core plucked out, until Mujō Bushi sought it out and killed it with his own hands. Mujō Bushi was another idiot who had thought his subpar skills could bring him to face the entire world.
