“2,000 were with Saul in Michmash.” Saul lost that hilltop to the Philistines, as we see by 1 Samuel 13:5. He retreated southeast to Gilgal (1 Sam. 13:4). Jonathan had to retake it (cp. 1 Sam. 14:5).
“and 1,000 were with Jonathan in Gibeah.” Verses such as this show that when Saul started to reign he was a mature man and had a fully grown son.