A .003 SG difference could simply be the variation in refractometers or test equipment. The accuracy of a Milwaukee digital refractometer is +/- .002 SG. I would expect the accuracy of a refractometer would be even less. In all likelihood, their test equipment is reporting 1.025 SG on their tanks. If they tested your tank, they would probably read 1.028. Either way, both SG are totally acceptable and well within standards for fish and coral. To me, a .003 difference wouldn't concern me when acclimating new fish or coral. It's not like the store was running hypo salinity at 1.008-1.010 SG and telling you it's 1.025 SG. Honestly, I would be looking elsewhere for the cause of the death of your fish and coral. If all parameters are in check as your signature implies, they may have died simply from the stress of being plucked from the ocean, flown thousands of miles, handled, treated, dipped, dumped, and from moving between less than ideal living conditions on their travels to your house. That seems to be a common culprit when everything else checks out.
Disclaimer: I don't know what store you are referring to. Just providing my experience.
Also, it may be worth taking your refractometer to the store and testing salinity side by side. Maybe your refractometer isn't calibrated properly? I don't know a single LFS that would be offended with a customer trying to compare/calibrate their test equipment.