If I see a flock of geese fly by me then a few seconds later, another. What exactly is the proper way to describe that?
I saw two flocks of geese?
I saw a flock of geese, then another?
Saying “two flocks” just sounds odd, but perhaps that is the correct way. Anyone?
You saw two flocks of geese.
Why does that sound odd?
Flock is already plural, so adding a number in front of that just seems odd. You never say “I saw two deers”. Seems the same thing to me.
Flock is not plural. It is a singular noun that refers to a collection of geese.
If you’re still confused, try substituting the word group instead of flock in your sentences and see if it sounds any better.
Flock is singular - it’s a collective noun. It’s no more incorrect to “see flocks” than to “see orchestras”. ‘Deer’ is entirely different, because the singular and plural of the noun are the same. (How about ‘flocks of sheep’? 
)
I would have thought that “flock” isn’t plural; it’s collective.
It’s not the same as “deer” - you can say:
I saw a deer
I saw some deer
I saw two deer
And you can say, “I saw a flock.”
But you wouldn’t say:
I saw some flock
I saw two flock
I don’t see any problem at all with “I saw two flocks of geese.”
It’s not the same thing at all. “Flock” is singular. It describes one thing, a flock. Now this one thing might comprise lots of other things, but that doesn’t make it plural (unless you’re British 
).
Is “confederation” plural? What about “neighborhood”? What about “congregation”? These are all things with multiple elements, but they are all singular.
It’s got nothing to do with “deer.” “Deer” is one of those strange words whose singular and plural forms are identical. Try substituting a non-irregular noun, like “dog.”