Dany didn't do anything worthy of distrust in last episode, but her conduct after winning the new Burning Fields *could* be where Tyrion and Varys start to get leery. Her preview intimidation of Jon Snow and her lines while accepting the surrender of the troops could imply she starts to take too firm of a hand towards both her defeated enemies and potential allies-- not necessarily in regards to her conquering the Seven Kingdoms, but in regards to her ruling them.
Sociologically speaking, a decent chunk of the damage the Lannisters have inflicted upon the realm is towards the political and societal infrastructure; not only have they, and unfortunately Dany, wrecked up the material food supplies of the continent, their actions towards the feudal lords and common folk have damaged the stability and interconnectedness of the realm. Towns and villages are less likely to trade with each other if they think a rapacious army is going to come through, see you traded with someone they don't like, and kill you, or see that you have stuff they want and they don't want to trade with you, and kill you.
Dany *could* risk worsening that damage if she recklessly burns everyone who refuses to immediately bend the knee. She needs to have enough finesse and patience for diplomacy, especially if she wants to avoid more risks to her inheritance. If you kill off all the wary lords before talking to them, you can't control the Kingdoms.
More specifically, it could be that Varys and Tyrion look at Dany being a little capricious towards Lannister and Tarly holdouts, and worry she'll start applying the screws to Jon. Jon's objections to bending the knee are *not* about his pride. It's about his people in the North refusing to follow a Southerner's orders, when they need the South's support for the Long Night. Killing Jon could permanently lose the North for Dany; the books make it clear that tiny little Dorne managed a decentralized resistance tough enough that dragons died, and the North is basically Dorne with the size of the rest of the Kingdoms.