"Men don't cry for themselves but for their comrades". Angeal's death left a huge impact on Zack, Aerith was there to comfort him.
Cissnei's friendship with Zack taking priority over her orders to eliminate him.
When Sephiroth gives Zack permission to return to Midgar because there are reports of monsters in the slums — it's pretty clear that Sephiroth knows that Zack would be worried about his girlfriend (even if Sephiroth doesn't explicitly know that it's Aerith). That faintest hint of an indulgent smile on Sephiroth's face as Sephiroth reassures a flustered Zack that they'll meet again soon....
Additionally, Sephiroth notes when he arrives on the scene that he was on his way to Modeoheim, but diverted to Junon when he heard Zack was there. He delayed arrival at his assignment just to stop by and tell Zack the situation, and let him know he should head home to make sure Aerith is safe.