So, at the start of the 24 hours of Day 3 we learn Kyle has been hired to traffic some cocaine from somewhere in Mexico to California, it's then implied that the cocaine is contaminated with the Cordilla virus. When his house is raided and his mother attempts to flush it down the toilet, the CDC runs some tests and determine that the powder is harmless: neither drugs nor the virus.

At this point, it's then implied that Kyle is himself infected with it, and thugs hired by the Salazars capture him and put him in a containment chamber so they can extract it from him. The hired people certainly act like he's dangerous: they scrub themselves down and throw away all their clothes and such, so I get that they believe it. However after Kyle is retrieved it's revealed he was never infected and it was just part of Jack and Hector's plan to get Ramon released from prison.

But if this is the case, then why would the Salazars expend resources to try and track down Kyle? They know they don't have the virus (as they haven't bought it yet), so when Kyle was running away from the cops, why would they bother to intervene instead of just letting him run away from CTU?

You could certainly argue that it was about wasting their time, but it would have been just as effective without Kyle, they already dumped the body, they could just claim to have a way of releasing it and the authorities would spend all their time looking for a lead which doesn't exist.

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