I've had some collections where all the eggs get counted into my inventory and other times when they don't. Twice yesterday, I should have received six eggs (4+2), but only 4 counted towards my inventory. I was unsure if this was happening because I hadn't exactly checked my egg count before I collected. When I did a third collection, it correctly counted the eggs.
But today it definitely happened. I had 40 eggs before my most recent collection. Now I collected 6+4 (pop-ups shown when you collect from the swans) and yet I only have 46 pink eggs.
I've tried completely closing the game and reopening it to see if those eggs would appear in my inventory and they haven't.
Edit: I collected again. Supposedly 4 eggs and 2 eggs, but my count is now at 50. Not the biggest problem because there is a lot of time left, but those missing pinks will eventually add up to the cost of one of the animals.