Seems like a simple fix. I'm guessing column names aren't being bracketed on some SQL create scripts. Error occurs on a column called 'Order' when I annotate an index in my mapping file:

Property(e => e.Order).IsRequired().HasColumnAnnotation(IndexAnnotation.AnnotationName, new IndexAnnotation(new IndexAttribute("IX_MacroStepOrderDuplicate") { IsUnique = true }));

The problem goes away if I remove the column annotation.