Its strange how they portray indou as dense about attraction but perceptive of everything else, and then also good with natural instinct. It doesn't feel like it really fits together wel
As others have said, Indou is exceptionally smart (her aunt says so, and she’s no flatterer) but untutored and unsocialized (so far). And we now know that she takes after her highly respected and competent mother.
Indou apparently has been raised in rural and poverty-stricken isolation, so she had no experience at reading anything like Kagami’s mixed emotional signals.
That’s a quality Indou shares with half the readership, it seems, who decided on the basis of Chapter 1 that Kagami was a demon from hell despite the blatant signals that, although she is sharp-tongued and strict on the surface, she is actually generous and kind-hearted.