i can not reproduce that:
e.g. population: 13, happiness: 100%, raw science: 27.5
joeball123 explained it well, thank to him.
My suggestion for the functioning of Projects:
I would prefer a solution where the different projects are completely disassociated from the manufacturing production setting (the planet production "slider" setting (the "wheel") for % of manufacturing), and act as independent bonuses.
They should give flat and % bonuses in a way of complementarity, flat bonus for the improvements with % bonus, % bonus for the improvements with flat bonus (or even % and flat bonuses at the same time in some cases), and, perhaps (but not fundamentally needed), then be modified by the Population on the planet (more population, greater bonus).
Example: (all numbers are for explanation only)
Research Project: +2 points (flat bonus to act with the % from the improvements (but can be flat and % bonus at the same time)) of research ("similar" to raw production) x Population/10
For 10B Population, with 100 % bonus from improvements:
Research Project: (2 x 100 %) x (10 / 10) = 2
--> 2 points of "final research points", not modified by the planet production setting (the "wheel"), thus completely independent.
For 100B Population, with 100 % bonus from improvements:
Research Project: (2 x 100 %) x (100 / 10) = 20
For 100B Population, with 1000 % bonus from improvements:
Research Project: (2 x 1000 %) x (100 / 10) = 200
So, the Research Project is only influenced by the Research improvements built on the planet, and perhaps also by the Population (to make it different for each planet, and more fun to use).
And the same for the others types of projects.
And, when there is no improvement and no ship to be built, the manufacturing points generated (the "wheel" setting) are directly redirected to Research and Wealth (with some penalties), in consistency with the player's settings for Research and Wealth (the player's setting is conserved and readjusted when there is again improvement or ship to be built).
So, the manufacturing bonuses become a small part of research and wealth bonuses (it's not overpowered), it's entirely automatic (less micromanagement), and the player is not surprised by a misleading process (when he adjusts the planet production, it works as expected).