Airlines sell tickets through multiple channels (both online and offline), and they are not required to verify each passenger’s eligibility for entry or transit.
Moreover, it’s impossible to reliably check entry requirements for each individual passenger automatically. For instance, had you been an Indonesian citizen or resident with the same ticket, perhaps you would have been allowed to transit. Even check-in agents can get this task wrong and occasionally need to ask superiors or wrongly refuse people.
If there is a warning on the website, it’s usually generic, along the lines of “the passenger is responsible to comply with any entry or transit requirements”.
Your best bet is to ask the airline to reschedule your flight or rebook you on a different itinerary. One time, British Airways rebooked me for free when my ineligibility to transfer was discovered upon check-in. However, this is a courtesy, not an obligation, so make sure to ask nicely.