Which is the cause of "scan losses" in a linear phased antenna array?
Array factor does not show scan loss. Array factor is merely a multiplier. It's actually a common mistake for engineers to use the array factor as a gain value. Array factor gain does not change with scan angle or element spacing!
To see scan loss, you need to calculate the directivity. However, for a uniform linear array (ULA) of isotropic elements you will not see any scan loss when you calculate directivity. You need to either use a 2-D array or use a non-isotropic element pattern.
Physically speaking, a loss in directivity is caused due to less effective area pointing in the direction of interest. Scan loss occurs when the array has area (e.g. not an isotropic ULA).