I think Kagami is more the one with the problem than Indou.
Indou is experiencing something for the first time and is trying to work out how to handle it.
Kagami, on the other hand, seems to have a genuine issue that is not yet addressed. She obviously likes Indou as she has said as much, so perhaps it is due to her rank or something else. And nah, I've not read the spoilers, so don't direct me to them. I like to be surprised! :)