This area of partnership tax is complicated and I am sure that the preparer of the tax return is a Big 4 Firm that has done this a time or two (or is at least reviewing the return).
Having said that, individuals make mistakes.
However, you are not comparing apples and apples between the two K-1's. When the "built-in gain" box is checked on a K-1, this is determined based on FMV at the date of contribution (where FMV is greater than adjusted tax basis) which will not agree with the "old" K-1 books and records. Essentially the assets were booked up as a result of this event. The preparer of the tax return will handle any Section 704(c) implications from this book up event and will run those through the "new" K-1 on line 1 (or appropriate line).