Shaking/Inverting the Vaccine Vial

At a guess, shaking it may heat up the liquid marginally resulting in it potentially being non-viable.

It could also result in small amount of particulate coming off the cap of the bottle into the solution, or could cause part of the solution to separate resulting in an unequal distribution?

In terms of the two doses you saw, it may just be the difference between diluted -v- undiluted.