Berachos 30b

Gemara: "R' Yochanan said, 'I saw R' Yanai pray, and then pray again, [so it must be that he said Musaf by himself.]' R' Yirmiyah said to R' Zayra, 'Maybe [R' Yanai] didn't have proper kavanah the first time, and he repeated his davening because of it.' R' Zayra answered, 'Look at the great man who testified about him.' " In other words, R' Yochanan certainly knew what he saw when he testified about R' Yanai.
One could ask on this gemara from the gemara later on, on 33b: "One who recites the Shema, and repeats it is shameful... R' Pappa said to Abaya, 'Maybe the first time he didn't have the proper kavanah, and that's why he repeated the Shema, to say it with the prioper kavanah.' Abaya answered, 'Is one a friend of Hashem? [May one speak to Hashem like he would to his friend?] If he doesn't have kavanah the first time, we hit him with a blacksmith's mallet until he has kavanah.' " Now, Abaya presumably wasn't saying that we actually hit him (it's hard to have kavanah when being hit with a mallet!), rather he was putting the importance of having kavanah into perspective for R' Pappa. However, we do see how unthinkable not having kavanah is - even to a regular person (because Abaya and R' Pappa weren't talking specifically about great scholars). If so, what was R' Yirmiyah thinking when he asked that maybe R' Yanai didn't have kavanah? Also, why didn't R' Zayra answer that it's unthinkable that R' Yanai didn't have kavanah?