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It is scratch resistant not scratch proof - In order for your phone to be or have deep scratched then something must have been of the same hardness or harder to have done that
Now it is a bit too late but I would suggest you to buy some kind of screen protector and the same for back.
Z1 has ASF protector on top of itself with embedded Sony logo. The problem is that despite Dragontrail glass below it is quite easy to scratch the ASF even if you try to avoid anything hard.
You may try to remove ASF but you will lose warranty, fingerprint protection and Sony logo.
I'm not sure but try to call Xperia Care. Maybe authorised service center can do something about it (at some cost of course) and then you will apply additional screen protector yourself.