Well I'm having the same issue with not being able to close the skill tree. I did close it by clicking on the phone's love interest heart app (while in MC's room), but as soon as you try to talk to the guy sitting on the floor...the skill tree comes back. And when you try to close it again using the method I mentioned above, it sends MC back into his room (like it's resetting MC's location). (Sigh, sandbox and mini games, two things I really dislike...Right up there with NTR, predatory lesbianism and forced sharing.)
And a suggestion for an issue or potential issue that I noticed...there are no labels on any of the doors (mouse over labels that let the player know room details...like most other sandbox title do).
And I'd suggest there should be a default superhero name, or allow the player to get to know what powers MC will or has before there is a forced "pick a superhero name" choice.
Anyways, I believe due the sandbox / phone coding...this title has some game ending bugs.
Wish the dev good luck with this endeavor... I'll check back if and when these issues have been resolved.
Regards.