This seems to have been a problem for a long time (several years and numerous versions of Quicken - I've been a user since 2007), based on my own experience and other threads I've seen.
Please send this feedback directly to actual developers.
The problem is not that multiple logins are used for the same financial institution; I have cases where my spouse and I both have our own logins and accounts at the same bank, and those accounts are added/updated without issue.
The problem comes from having the same employer. Fidelity (and maybe others?) use a common plan number as an account number for all employees on a specific employer's plan. So even though my spouse and I have different accounts and different logins, the "account number" sent by Fidelity and stored in Quicken is the same, because we are both members of the same 403(b) plan that our common employer has.
Behind the scenes, you will need to update Quicken so that it uses a combination of Account Number and Customer ID to uniquely identify an account. Right now, it appears that the software is using Account Number only, and then struggles to behave correctly when that turns out to be not unique.
I look forward to finally having this ridiculous issue resolved.