That line was referencing a deleted scene in which Obi-Wan talked to Padme about his worries about Anakin (which would’ve actually been a great scene from what I read in the script had it been left in; the dialogue is actually fantastic, you can read it on Internet Movie Script Database), not Obi-Wan and Padme having an affair.

In the novel that delves into what Palpatine made Anakin think what was going on, it wasn’t an affair either: he was trying to convince him that the Delegation of 2000 and the Jedi were teaming up to overthrow the Republic.