When you take the bottle out of the fridge, it is recommended that you swirl the milk rather than shake it. This is because shaking it can denature the amino acids. Same with freezing or boiling the milk. The milk's still good even if you've shaken it, it's just better if you swirl Here is a link to an article about this (non-LLL source)
Shaking or swirling, though, won't affect the calorie and fat content of the milk. As long as your LO is drinking the whole thing, then they're getting all the good stuff.
As long as your LO is gaining within the wide range of normal and having enough wet and poopy diapers you're fine
Hope that helps!