In Otoufu land, they just have personalities that naturally clash. Ikazuchi, Commander reliance aside, is a girl with a forceful personality who doesn't hold herself back from doing or saying what she thinks that mixes with 'Bono's own cantankerous nature like dogs and cats.
(In fact, I'm pretty sure that diary entry is just joking about how they can be "heading in the same direction" (agreeing with one another) one day, then "opposing directions" (arguing with each other) the next for nearly no reason.)
Updated
I sorta felt like a torpedo.
(In the torpedo tube.)You're fine outside it, aren't you?
You'll only make us wet!Heeeeey!
Save uuuuus!*SQUEEEEEZE!*AH!LET US IIIIN!Hold it!
Wai--!I was gathering shellfish on the beach when it started raining❤ Let me in.What the heck were you doing there?!!*Siiiiigh*