So, let me restate this to make sure I understand.
This problem happens when you answer the question on your wife's HSA "I was covered by an HDHP during at least one month during 2017" as Self instead of Family for the first 6 months of 2017, right?
When you hit the Calculate Max Contribution limit button, what was the answer?
Your wife contributed nothing to her HSA in 2017, right?
When your wife had the question, "Was [name] covered by a High Deductible Health Plan (HDHP) in 2016?", did she (you) answer "Self"? and on the subsequent screens did you indicate that she had Self coverage every month in 2016?
Did your wife report an "overfunding" of her HSA in 2016?
You have seen the HSA Summary screen, right? What are the differences between when you enter Family and when you enter Self?
