"This has caused us to issue incorrect refunds, and reduce  the following years estimated payments, only to discover the mistake and have a very upset client."

No, that is because the client did not give you that information and/or you did not ask for it.  It is not the program's responsibility to prompt you for everything.  The program won't 'prompt' you for other carry over things either, such as 1099-Rs or W-2s (unless the carryover W-2 has a carryover input in Box 12).  Again, it is your responsibility to know what needs to be entered, not the program's.