He wanted to comfort her. He wanted to ask her what was wrong and then viciously maim whoever had upset her. He wanted to gather her shaking form in his arms and hold her until her tears subsided.
But, he couldn’t do any of those things.
Because he was Draco Malfoy, and she was Hermione Granger, and they didn’t do those types of things.
So, he settled for watching while she cried for a reason unbeknownst to him, silently praying to whoever was listening that she’d just stop. Then maybe the terrible ache in his heart would subside.