So i went through the previous arcs:
Xenomorph arc: Atropos lies about pretty much anything involving the aliens
Clotho arc: Atropos hid the fact that one of the other station AI's could be activated (and also how much authority John actually has as the sole survivor)
Into the Breach: Atropos hid the whole existence of the zombies from both John and Clotho
Sepia: Atropos hid her part in killing most of the crew either before or after they became zombies (and she never did tell him about killing the captain)
Venting: Debatable, Atropos planned on not letting John back in and letting him die in space but didn't technically lie about it
Pirates: Atropos spends most of the time out of commission, avoiding lying by not taking part in the plot
Time duplicate: Atropos surprisingly is not lying to anyone about anything
Puppets: Atropos hides her puppet from John (though he admits he's happier not knowing

So yeah, Lying and hiding things from people is kind of Atropos' whole bag