Version 3.9.0 essentially changed the default reporting level for a host of Mixed issues.
In retrospect this was not the best idea – people saw a (non-error-related) number go up (because of all the newly-reported mixed issues), and people don't like numbers going up.
So this reverts that behaviour – any project that had totallyTyped="false" before will show the same errors & info as it did in 3.8.
This also introduces new flag reportMixedIssues (documented here) that allows more fine-grained control than totallyTyped offers.