I think this was hinted at when Lalo burst into their apartment to question Saul at the end of season 5. Lalo wanted to know what happened on the trip to recover his bail money, and Saul wouldn't tell him about Mike's involvement. Lalo was suspicious because the car he found was all shot up. Saul claimed he just drank his own pee after abandoning his car, and that it was just kids playing with guns in the desert that shot up his car after he got out.
The cup was evidence of his lie. Kim made a note of it earlier in that episode. If Lalo had seen the money bag with the shot-up cup inside, Saul's story would have been blown.
Now, at that point, they do think Lalo's dead, but, Kim is the kind to be methodical about covering tracks. It happened when the initial plan to frame Chuck for the typo on Mesa Verde's documents: just as they were going to sleep, she said something like, "Jimmy, you better have covered every single track and left no evidence", at which point he excused himself and ran to the copy shop to bribe the employee (and witnessed Chuck have a panic attack).