I somewhat noticed that Sayori and Junko almost have the same color eyes but there's a difference. 

Sayori's eyes are almost a sky blue color while Junko's eyes are almost a darker shade of blue.

I feel like Sayori gets her eyes from her sister but has a little more saturation. 

Yes, they were born from different wives. A'ghor and A'habbat but they have the same father.