Radak: Yirmeyah prayed for some (Anshei Anasos) for evil. They wanted to kill him; he said "I will see Your vengeance from them" (11:20), "make them like flock to slaughter, summons them for a day of killing" (12:3). Hashem forbids only praying for Yisrael for good.

Malbim: Sometimes Hashem punishes via hiding His face (Hashgachah), and the punishment comes by itself. When one prays about this, it is l'Tovah, that Hashem should not hide His face, rather, He should benefit them. Sometimes the punishment is via Hashgachah; Hashem Himself punishes. Then we pray that He not harm them. Then, fasting and Korbanos do not help, for the decree was sealed and great Teshuvah is needed. Yirmeyah thought that the punishment was the first way; he said "Al Tanichenu" (verse 9) - do not leave us to chance. Hashem said, do not pray l'Tovah - the punishment is through Hashem Himself.