We have faced these few issues within ERPNext:-
Migration and Rollback process is not well defined and design in ERPNext, which creates a big issues with Production Server.
Any change in previous Design and major Functionality change should validate existing Data on server which is also missing, results in Breakages of Production server.
Regular updates and changes required in Documentation part as well.
These all major changes results in data validation and data loss which is not acceptable in production servers.
I believe these are major pin points for every user of ERPNext, so decided to share with you. Hopefully you will consider it quickly.