The three main possibilities are: 1) One of you indeed brought a new infection into your relationship. I cannot judge that possibility; only you and your wife know the truth of your sexual histories. From my perspective as an STD expert, of course this is always my initial assumption. But I do not know you or the nature of your and your wife's sexual lives or fidelity to one another; you have to judge that yourself. If you haven't had sex with anyone else and are confident your wife has not, then this simply is not a possiblity and you can disregard it.
2) Your wife had a false positive test result. Depending on exactly which test was done, this could be a good bet or an unlikely one. Some of the older chlamydia tests (e.g., the Gen-Probe company's Pace II test) frequently give false positive results. The newer ones (PCR and related test techologies) do not commonly give false positive results, although to some extent this is possible with any lab test.
3) You or your wife has been carrying chlamydia since before your relationship began. The longest documented chlamydia carriage is 4 years. It's rare, but it happens. (In this case, it is possible that her earlier test missed a low-grade infection.)
The chlamydia and HPV issue are unrelated. And no, there is no way to catch chlamydia except sexually.
Bottom line: To be safe, both you and your wife need to be treated. If you and she are mutually confident in each other's fidelity, then one of the other 2 explanations has to be true. In that case, I suggest you forget the whole thing once you have been treated.
Good luck-- HHH, MD