You only have several possibilities to believe with this siruation.
Your wife is playing around
The Clamydia tests are not accurate and produce false positives
Or like someone said, sitting on a dirty workout bench at the gym..why not a toilet seat then?
Speaking of gyms --- I was once sitting in the whirlpool, feet only, and a babe in a postage sized suit sat beside me and also soaked her feet. She eventually told me that every time she gets all the way into the water she gets a weird infection. So if clamydia can survive ~110 degree water and whatever chemicals they put in whrilpools this can also be a source of the problmem.
From what you said, I would go with dirty instruments in the "free clinic" or poor lab results.