Pong Krell hadn’t fully given into the Dark Side. He planned to stay in the Jedi Order as long as he could to sabotage them from the inside. This led him to hide his betrayal very well. The reason no one suspected him could be the same that no one suspected Palpatine’s betrayal coming. The Jedi had lost their way and were blinded by the war. With so many things happening, Pong Krell’s scheme was easily missed.