@dokidoki The author (Hatsuki) originally was putting out this story for fun on twitter and pixiv. Later, when they got a deal to put out a volume, their editor gave them a bunch of suggestions for how to improve it for the print version. Hatsuki took the opportunity to dial up some parts of the story (bonding between characters) and downplay other parts (role of the dad, bed wetting, and other traumatic scenes). For this reason, the chapter numbers don't always line up during the first volume.
Personally I believe the best way to appreciate the series is, at least for the first volume, to read both versions, because they each offer something interesting.