According to Cars.com, two subcompacts—the 2000–2005 Toyota Echo, and the 2008–current Smart ForTwo—made it on their list of "Worst Cars of the 2000s."
The article says the Echo "just wasn't a very good car," and that it didn't attract many buyers. As for the ForTwo, they said the car didn't deliver on the benefits of being small. It didn't have great fuel economy, had an SUV-like propensity to roll over, and had a not-so-stellar transmission.
The full list included (in this order):
2001–2005 Pontiac Aztek
1999–2002 Daewoo products (all)
1999–2002 Isuzu VehiCROSS
2002–2008 Jaguar X-Type
1995–2005 Pontiac Sunfire
1997–2001 Cadillac Catera
2000–2005 Toyota Echo
2007–Current Jeep Compass
1995–Current Chrysler Sebring
2008–Current Smart ForTwo
Worst Cars of the 2000s (Cars.com)