If the game allows the player to do something you have to believe the player will do it. If player is allowed to enter more than one route at a time, the user will do it. It is the devs job to cover these cases by either making sure a user doesn't enter more than one route at a time or make sure user doesn't get bugs when they do."User" being only you bugging out in 3 different routes at once is still only you. And no1 else since before 2018. So yes, it's a you problem. Sandbox has nothing to do with anything if the game fucks itself when you go into 3+ routes at once, it doesn't if you go only 1 at a time. Shocking.
Try reporting it to the bugreport (you have to pay to gain access) and provide a save file. Either they'll laugh at you or find new bugs that no1 else managed to in ~4 years
These are fundamentals of project development taught in engineering course. If the dev is not familiar with it they can learn something new. Blaming the user because of oversight on the devs part is a fundamental mistake.
I am sure the dev knows his shit, they have made good decisions so far. His work is simple but fun and now they are going for code overhaul which will help them keep track of issues and make the development process easier.
If the community is laughing at anyone trying to share their experience and report bugs, they are, knowingly or unknowingly becoming a blockade to the development process. I hope the dev is smarter and listens to his players even if they are repeating what has already been mentioned or at least pretend.