Undercooking tofu causes a bad stomach. Is this true?
Firstly…  Do you think your girlfreinds may simply be worried about being gassy from eating beans? 



It is a misnomer that tofu is ever technically “raw” because because all the ingredients for making tofu are cooked (brought to a simmer or boil) in the manufacturing process.

The soymilk is often cooked twice when making tofu: first when making soymilk from soybeans and second when making tofu from the soymilk. (However the process of making silken tofu from soymilk does not always involve a second step with high temperatures.)

Some possible reasons that tofu could cause a bad stomach:


tofu is past it’s expiration date.
tofu was not refrigerated properly.
tofu is somehow contaminated.
allergies to soy.
eating beans can cause gas.


If it's the gas, try fermented soy products (such as tempeh) which cause much less or no gas.

References:


http://www.seriouseats.com/2011/08/how-to-make-fresh-silken-tofu-from-home.html
http://www.seriouseats.com/recipes/2011/08/fresh-silken-tofu-recipe.html
http://www.veggieboards.com/forum/21-general-food-discussions/14467-raw-tofu-safe-eat.html
https://www.westonaprice.org/health-topics/soy-alert/soy-carbohydrates-the-flatulence-factor/
https://therightplan.com/tofu-does-not-equal-eating-healthy/