"The HR person said that the employer contributions to the pension had to be taxed. Has anyone ever heard of that?"

Perhaps it is a nonqualified plan? Was it covered under ERISA?

"her contributions didn't get taxed in the rollover, but they said since she was vested in the pension plan, the amount contributed by the employer was taxable."

Okay, but then you either have basis going forward (Form 8606), or that could have been rolled to Roth. What a mess. So many variations. You might start here:

https://www.irs.gov/retirement-plans/plan-participant-employee/rollovers-of-retirement-plan-and-ira-...

And this chart:

https://www.irs.gov/pub/irs-tege/rollover_chart.pdf

You might ask around to find a mentor. It is possible you'll find another tax preparer who has clients from that same situation.