Sometimes techs don't stack to make the interface clearer. For instance the garrison techs i added are all mutually exclusive, so the troop strength meter says:
"Garrison 1: +10
Garrison 2: +10
Garrison 3: +20"
Similarly for growth techs probably one only ones that should be mutually exclusive are the ones that are supposed to be the same sort of thing.
It's quite possible that while removing redundant theories i broke the stacking exclusion for some techs. I usually kept the name of the theory, while deleting the name of the application, and giving the theory the application's effects.
I don't have much time today. If you want to investigate this further please feel free and report whatever else you find.
Xenological Hybrids and Xenological Genetics were supposed to have bonuses that didn't stack. I broke it earlier, but it should be fixed as of revision 4476.
EDIT2: The tunnels special was also effected. Fixed in revision 4478. Now i'm searching all files for references to removed techs.