It's been going on for a while.
If you have an account, you can go to your account settings, and under item 6 (Position-Only Flights), there is a toggle to either show or not show position-only flights. The note associated with that setting reads, "When this option is activated, you can see additional flights for which FlightAware does not have a filed flight plan.
Tracking data for position-only flights is incomplete and potentially inaccurate."
Even before this, some flights would appear without a flight plan. For instance, if you got flight following services, your flight might be available (but wasn't always).
Basically, FA consumes whatever data ATC feeds them, and they do what they can with it.
If that bothers you, check out their FAQ on the subject: flightaware.com/about/faq#blockmytail