I had the same issue with the biometrics letter for my mother in her visitor visa, where her first name appeared under the last name, and the last name was under the first name. I booked an appointment with VFS Global (VAC), they told me that they take the name from the passport, not from the visa application.
During her biometrics appointment, they used the name as it appears on my passport. After taking her biometrics, they updated her name in the system and gave her a biometrics confirmation receipt showing her correct name.
When I checked later, I saw that the IRCC had also updated her name according to the biometrics receipt from the VFS (VAC), and her biometrics had been successfully uploaded.
I hope this helps anyone who might face a similar issue in the future!
