Chapter 20 has Takao snuggling her Gunzou body pillow.
A bonus page in the seventh volume shows other assorted belongings of hers: books on strategy board games, do-it-yourself scale models of the original I-401 and Takao, a picnic set, a complete navy captain uniform set and Gunzou body pillow ver2.0 (now in casual clothes).
Takao and Gunzou shakes hands in Chapter 31. She manages to keep her composure until he turns around and then she just stares at her hand almost as if saying "I'm not washing this hand ever again".
And starting with the intro for Episode 6... Bear!Kirishima and Kirishima show up side-by-side.
Bear!Kirishima trying to swim in episode 8. Turns out that the plush body absorbed so much water that it renders Kirishima immobile when soaked enough. To remedy this, Haruna wrung the water out.
The ending of Episode 7 is completely identical to the normal ending... Except the Mental Models are replaced with the ships, complete with the orientation of each Fog.
Chapter 50 of the Manga has Iona temporarily in charge of... Herself (oh such shenanigans Anthropomorphization brings), when the Fog suddenly attacks while they are at depth, catching the crew totally off-guard, leading to this moment:
Iona: Start the engine! [...] 401! Slow to the side! Sou! Lock the doors that aren'talong Shizuka's path.
Iona: Kyohei! Insert corrosive warhead torpedoes into tubes 1-4! Insert active decoys into tubes 5 and 6!
Ashigara nearly drowns herself when she dives without putting up her Klein Field to go after 401.
Early in episode 11, Haruna remarked that losing Takao was a great loss... only for Takao to appear on several screens a few moments later (and finally being spun by Makie, complete with swirly eyes on Takao's end). This is quite a Mood Whiplash after episode 10's serious Heroic Sacrifice.
Episode 12. Takao's mental model is restored. Her very first action is to tackle Gunzou.