At one point I wondered if I was causing the final rankings to be messed up because sometimes I would do a sneak peek and simulate the NC before I would actually play my bowl game. I stopped doing that, thinking that might be causing it, but it's happened even without me prematurely simulating any games.
Here's something else that occurred at the end of my last season (year 2038), where it had Navy ranked #1, even though they lost the NC to Georgia.
I was #12 Oregon State, and I defeated #16 Texas A&M in the Holiday Bowl, 41-20. But in that same, bugged final ranking, I fell to #13. So
something shifted around and the game calculated some new final rankings, but obviously it didn't do it correctly.
This has jogged a memory from where I have posted about this exact scenario happening to me in the past: In year 2016, I was #16 Alabama, and I defeated #9 Michigan State in the bowl 34-31. Final rankings showed Michigan State actually rising to #8, and had me still at #16.
Anyway, not the biggest issue in the world, just a minor annoyance. You could be right that it could be an unavoidable or unpreventable bug.