Hi. when taking a stool test, can a minor urine infection make the test seem higher in inflammation than it might be?

Probably not: I'm not sure what type of stool test you are doing, but usually stool tests are done to check for internal bleeding or the presence of infections ( parasites or specific intestinal bacterial infections such as shigella, salmonella, or campylobacter). The only possible effect a urine infection could have is if you have blood in the urine and some of the urine ends up in the stool container.