I agree... Kail... love the mystery, and I loved not being in the know.
My logical mind says it's far fetched, like when the clocks are all wrong or mis-match to when they next email Starfleet. But I don't care too much... love the mystery.
And I like the ending, where we feel we share a secret with Data.
And why would the aliens do what they did? Well much like the Prime Directive they'll have their rules, but can interpret it in many possible ways.
Edit to respond to startrekwatcher's comments: I agree, good analysis. I do wonder if sometimes having to official review an episode makes one more critical. And episodes like Clues will never hold up as greats in terms of pivotal or groundbreaking stories, they are fun and enjoyable and shouldn't be scrutinised too hard.