The trace is shown as a thin line in the "Unrouted" layer.
Which means, they aren't connected physically.
While working through the eagle project for the Arduino Uno Rev 3 Reference Design I noticed that the track connecting Z1 to L1 is missing in the PCB project. Can somebody please confirm this and if it is correct.
Yes I see the same thing, which is not present in the initial rev (R1?) of the Uno design.
The broken track however does not appear to be present in the Arduino Uno sitting on my desk..
This is just a personal belief: I believe subtle errors like this one are present in the reference design to throw off clone makers who just take the files and produce them verbatim. Maybe it was just a mistake, maybe it was intentional.