Much like life, many of the experiences in Mushroom Musume are fleeting things. Most of the things the dev team consider 'completable' are done through the final challenges you can decide on near the end of a run, otherwise don't worry about it too much.
(That said, this is something we're keeping in mind as we work on future updates! Both in the sense that there's some continuations we have planned of non-completed story stuff, and also we want to add more ways for players to feel in control of their playthroughs.)