Your post contains multiple spoilers to the current 6otM game. You should use the spoiler tag.
You can mouse over your science gen to get a breakdown of beaker sources. That alone might be able to show you the difference between what you've calculated and what the game is displaying.
In fact, I'm now left wondering why the faith output in the city is so high. The holy site and buildings account for 13 faith, with Old God Obelisk +4 faith, and Hagia Sophia +4. There are 17 faith from worked tiles that I can see. There is +30 faith from relics, and city-state bonus would add +3. So I get a calculated faith output for the city of 71, which also seems quite a bit off from the reported 92.
I dunno, I guess I'm overlooking some things but I still can't seem to account for everything I'm seeing.
When you can no longer gain a great person in a particular category, all GPP instead generate faith, so for instance once all Great prophets have been claimed, any building or wonder which would generate Great Prophet points instead generates that amount in faith in the city.
Another source of science is worked tiles, especially late when you have aquariums (science from reefs+coastal resources), zoos (science from jungle). Not a ton, but it can add up. Also trade routes can definitely be a source - again, often small values add up. Getting 1-2 science per trade route from sending to a city with a campus X 10-12 trade routes adds up, even more if you add in Pingala's multipliers. Another multiplier is happiness - 10% here or 10% there can add up too.