https://official-complete-2.eorzea.us/manga/Bleach/0407-015.png
^Here, the very first thing isshin notes is that he can't feel kototsu's presence, implying that he'd normally expect to detect its spirit energy, which makes sense as he was an experienced captain and likely used the dangai a lot.
Also isshin couldn't sense chrysalis aizen's energy so it'd absolutely make no sense for him to be able to sense post-chrysalis aizen's energy, hell this is even confirmed by isshin himself which is why he decided to train ichigo as he had the best chance of beating aizen since he could sense his SE:
https://official-complete-2.eorzea.us/manga/Bleach/0407-008.png
As such, the most likely explanation is that the residual spirit energy that isshin was talking about was kototsu's as we know in bleach that when you die your spirit energy doesn't instantly disappear and can linger around for some time before diffusing completely. This is shown when halibel could sense yammy's residual energy after he died in one of the novels (the one in Unmasked IIRC).
Btw I also offered the interpretation that gin's statement could've just been hyperbolic and thus there would be no conflict between what was said in the isshin/ichigo scene.