Ambiguous column error on single table
It's not precisely because there are duplicate entries in the SELECT list, it's because the ORDER BY mentions a column that is listed twice in the SELECT list, and SQL Server doesn't know which one you mean (think about the case where you could say SELECT ID, ID = 1-ID..., where which one you mean is important).

The right fix is (in order of my personal preference):


remove the second instance of ID
give the second instance of ID a different alias (like RedundantID)
use ordinal - ORDER BY 1 (would work, but definitely not recommended)


If you can't fix the code in the app, and can't get support from the vendor, I'm not sure there's much else you can do except move back to the copy of the database running on a version that can run in the ancient compatibility level required to support this syntax.