Altium Short Circuit Undetected Between Layer
I would guess you have your DRC (design rule check) set to only show shorts when the checker is run in BATCH mode. If you want to change this to also check in ONLINE mode you need to go to Tools --> Design Rule Check --> Rules To Check and check both boxes next to "Short-Circuit". 

You need to make sure that the design rule check is set to report short circuit errors, and that you don't have any rules that tell it to ignore the errors. 

It doesn't look like you reviewed your board a whole lot before submitting it. That's incredibly unprofessional and I'm not surprised you got this error. When designing PCBs it's always a good idea to not only check it yourself (with a long break between the initial design and when you review it again) but also have another PCB designer review it. For example, what's with that wacky bump in VDD_EXT_UG96?