I had the same issue yesterday.
In the morning I had a pink basket full, clicked on it and it only gave me 200 eggs.
Later that evening I had another pink basket full and again it only gave me 200 eggs.
I was pissed to logged out.
Then forgot that I had to harvest Carrots and when I logged back in my egg total went up 200 eggs.
So, for the 1st basket I only got 200 eggs but the 2nd one actually gave my 400. (but I had to log out and then log back in)
so, for now on when I decide to collect my baskets I'm watching to see what it gives me and if it gives me 200 eggs, I'm logging out and then logging back in. I'm also taking screen shots so if I don't get my 400 total I'm EA support. I heard they are sorta helpful.