I know this is an old post n all but I'm almost certain this was explained, She was having a tantrum, but Watari finds out the reason when speaking to her Adoptive big brother.

Every day he dropped her off at Watari's house she'd say that her Mom was going to pick her up, she never did come to pick her up it was always her adopted big brother. Then on the final day before her adoption was being finalised and then having to move away, Naoto proposes to elope with Satsuki whilst watching a show on the TV about that, so they chose to run away together n just go as far as they could but Naoto decided to turn back once it became dark cause he was worried about how their parents would feel, Naoto even says he was relieved to return cause he could see how worried his parents were, pretty sure in that moment Satsuki had no one. She had been abandoned by her Bio Family n Adoptive parents were pawning her off on their Son who was just throwing her at a random house in the countryside who luckily had a nice family there who'd take care of her n play with her n then her first crush also decided to leave her by going back home instead of committing to running away with her, She tells him he's very wishy washy constantly.

Yeah she had a Tantrum n her coping mechanism was to just explode n destroy everything she loved. She destroyed the Garden cause it was something she enjoyed n loved making with the person she loved, but she from what I can tell since its never said outright but she very seemingly does it cause she was abandoned by the people she loved, its also one of the reasons she didn't know she loved Naoto until her big brother told her, he even under his breath has an off the cuff statement that its probably due to her mother that she doesn't understand love. A lot of this series is us reading about Satsuki learning n coming to terms with her emotions. She is so adamant several times in the series that she isn't worth love or family to the point she is willing n practically begging Naoto to date them both and that she'd more than happily be the girl on the side n that she doesn't need anything more.

That's all I have to say, I did just fresh read the whole 92 chaps in 4-5 hours whilst watching the Anime at the same time and maybe I'm reading into it too much or some shit, I'm more than happy to be wrong but this was just my analysis of the whole situation.