Should I have been charged a 6% tax on a backdoor Roth conversion? We do it every year, and 2021 was the first time this has happened?

There is no problem with the software.  You either mistakenly reported a Roth IRA contribution instead of a traditional IRA contribution or the traditional IRA contribution that you reported was itself an excess contribution due to having insufficient compensation to support the contribution.

Which part of Form 5329 shows the excess contribution and calculation of the penalty?  The answer will indicate which of these mistakes you made.