Microsoft has been under attack by state actors for decades now, their security teams work hard to keep things together but even a company like Microsoft will fail when literally every large country is attacking them 24/7, including going so far as to get spies hired into the company.
Microsoft was historically very locked down internally, unlike Google where all source code was visible to everyone, Microsoft had (may have changed not sure) product code based cordoned off.
As for bypassing TOTP, does TOTP provide any security if running on a cell phone and the cell phone is rootkitted?
Microsoft had its signing key taken by the Chinese. That simply shouldn't be possible. They have repeatedly had breaches and in some cases comically bad holes in azure / email products / internal corporate products etc etc
Hence there is seemingly some other weakness allowing login to a corporate Microsoft e-mail account. For example, a method to enrol a second/additional TOTP generator by only knowing an account password and not needing to supply an existing TOTP code. Or a "lost my phone that generates TOTP codes" recovery process. Or for example, a Kerberos ticket accepted by Exchange can be obtained using a method that only needs a valid password and not a TOTP code?
Why the hence? Why not just root some MS employees not fully patched android phone while they cross a border?
Or just bribe an intern.