I have the same problem. On Mercy I have 600 hours playtime - yet I am only at level 28!? And this is not the only hero, I am missing around 1000 hours of playtime together on different heroes.
I opened a ticket and got the reply to write a Bug Report. The GM also send me a link to this Blue Post: Overwatch 2 Known Issues - September 4, 2025
I guess they are aware of the problem and hope they will fix it soon.