Eventually:
Here is a broken-down list of specific times where, Laeirthe is claiming, Merrin felt uneasy or uncomfortable or worried, and then forgot about it or declared it not worth spending more time thinking about as soon as she could reasonably get away with that.
1. The inexplicable language barrier. The abrupt lifting of the inexplicable language barrier, followed by some bizarre word choices that Merrin also doesn’t think resembled the usual, expected disfluency from after a resolving neurological-injury-caused aphasia, and instead - hmm, does Laeirthe in fact know how these things work well enough to draw conclusions - (low-confidence flag) that resembled someone who was, somehow, trying to express normal dath ilani concepts in normal Baseline when neither was fully familiar or comfortable?
2. Laeirthe thinks that Merrin might just be flat-out wrong to expect the Estha she knows to have performed better overall, on arrival to a strange planet, but it does seem like Merrin felt confused and uneasy about something there? Laeirthe's argument here isn't that her unease was valid, just that the grounds on which she ignored it were suspiciously motivated-reasoning-shaped.
3. Estha was confidently claiming in quite a pushy way to be less susceptible to mind-control than Merrin, while himself seeming rather impaired?
4. Merrin chose to question him on his memory of her True Death, on the grounds that this was a useful cognitive assessment for amnesia, and he in fact didn't remember it, and his explanation for what happened instead was throwing all of Laeirthe’s “that’s a load of flaming crap” suspicion alarms. Which might, to be clear, be miscalibrated here! Laeirthe has priors shaped from paranoia and paranoia is not necessarily in all cases truth-tracking! He doesn't confidently know that Merrin's memory is the true one, here, just - Merrin did run a test and did find the result concerning and then just sort of dropped thinking about it?
5. The vibes were off. Laeirthe is to be clear, not himself qualified to speak on that, but Merrin was troubled by it, and Merrin would know! She had an intimate relationship with the man! “Interpersonal vibes” may not be a type of evidence that Laeirthe is personally inclined to put much weight on, but Merrin seems to in general put some trust in her ability to tell what’s going on with someone. Apparently it’s relevant to her job or something? And she thought something was wrong.