I have a similar issue using the online TT Deluxe. Refinanced a $647k mortgage, then the mortgage got transferred so I ended up with three 1098s. Entered all three correctly, got the “error” where the box to limit interest was checked YES. So I went back and deleted the 1098s and re-entered. Same error. Unfortunately, when the software called for me to fix, I erroneously typed $0 and royally screwed up my return. Ended up calling support and after much ado, the rep found this. It is definitely a bug. Now I wait for a fix....
https://ttlc.intuit.com/community/payroll-reminders/help/check-this-entry-tax-and-interest-deduction...
