1)
Here he laments Yehonason alone. Why does he say "Naflu Giborim"?
1.
Malbim: This refers to the Giborim around Yehonason. They did not flee, and were killed with him. Sha'ul's Giborim fled, and were killed later.
2)
What is the meaning of "Al Bamosecha Chalal"?
1.
Rashi citing Targum Yonasan: You were killed on your strong place.