In Warranty / Out of Warranty confusion

Good day, <br> On the 7th August 2015 I booked in my Sony Xperia Z1 at the Vodacom Store in Parow knowing it will be sent to Somerset West and then on to Gauteng for any needed repairs. The speaker grill at the bottom of the unit and the one rubber seal on the charging flap was lost. I also requested them to look at the camera and LCD. On my online profile it was deemed an in Warranty repair which I did not question. Job number ***0<br> <br> I received an sms to collect my phone from the Parow depot on the 25th Aug, which I did. Upon checking the phone out, I noticed that the LCD was still the same and the camera was still doing the same as what I reported to be looked at. I booked it in immediately without taking possession of the phone. I did not even insert my SIM. Job Number ***4. <br> <br> This time when it reached JHB it was deemed out of warranty with a quote, due to physical damage, which makes no sense as the phone was in the same physical state when I booked it in the first time and repairs was carried out in warranty.<br> <br> Does physical damage only cover certain parts/repairs on the phone?