According to the film's official novelisation, Mace Windu and Master Yoda have been discussing the possibility of someone close to the Chancellor being a Sith Lord, in line with Dooku's admission in the previous film.
With what could only be described as a truly stunning lack of judgement, they ruled Palpatine out of consideration almost immediately, reasoning that he's too powerful to be a truly bad guy or he'd have already done something bad.
There's no indication that at the earlier meeting (in AotC) that they had any serious suspicions that Palpatine was a dark Force user or that he was anything other than a power-hungry politician par excellence.
“But he doesn’t have the authority to interfere with a Jedi
investigation …” Obi-Wan frowned, suddenly uncertain. “Does he?”
“The Senate has surrendered so much power, it’s hard to say where his
“It’s that bad?”
Mace’s jaw locked. “The only reason Palpatine’s not a suspect is
because he already rules the galaxy.”
“But we are closer than we have ever been to rooting out the Sith,”
Obi-Wan said slowly. “That can only be good news. I would think that
Anakin’s friendship with Palpatine could be of use to us in this-he
has the kind of access to Palpatine that other Jedi might only dream
of. Their friendship is an asset, not a danger.”
“You can’t tell him.” “I beg your pardon?”
“Of the whole Council, only Yoda and myself know how deep this
actually goes. And now you. I have decided to share this with you
because you are in the best situation to watch Anakin. Watch him.
“We-” Obi-Wan shook his head helplessly. “We don’t keep secrets from