It's not very common, but some computers use two different connections at the same time. Sometimes this is on a server or similar PC with multiple interfaces for extra bandwidth or redundancy, or maybe a laptop with both a 3G and Wi-fi active.

Speedtest.net uses HTTP to conduct the test, so the connection that it uses will depend on OS-level settings. Unfortunately, in our research we haven't found an easy way to force HTTP traffic to use a specific interface on either Windows or Linux, and this isn't an issue unique to our site. We recommend temporarily disabling other interfaces to force Speedtest.net to use a specific interface during testing.