וּקְרָ֣א עָלֶ֑יהָ כִּֽי־עָלְתָ֥ה רָעָתָ֖ם לְפָנָֽי׃
וִּקְרָ֤א אֵלֶ֙יהָ֙ אֶת־הַקְּרִיאָ֔ה אֲשֶׁ֥ר אָנֹכִ֖י דֹּבֵ֥ר אֵלֶֽיךָ׃
There is a difference in preposition between these two verses. 1:2 uses the preposition עַל whereas 3:2 uses אֶל. Scholars differ about the significance.
In 1:2 we are told the reason for the message – it is because Nineveh’s sin has come up before God, and therefore God’s message is against that sin. (I’m taking the כִי clause as the cause of Jonah’s message (‘because…’) rather than the content of it (‘that…’).)
Whereas in 3:2 there is a parallel going on which isn’t present in 1:2. Jonah is to קרא the message אֶל the Ninevites which God spoke אֶל him. Jonah is simply called to pass on the message which he has received. He is God’s prophet – God’s mouth piece.
Although these two verses/sections are clearly parallel, I think they are telling us different things. 1:2 is telling us the reason for the message; 3:2 is telling us (and Jonah) the source of the message.
1:2 tells us the content of the message; 3:2 tells us the source.
So no wonder different prepositions are used.