In The Name of Allah, The Most Merciful, The Bestower of Mercy.

فَلَمَّا جَآءَهُم بِٱلۡحَقِّ مِنۡ عِندِنَا قَالُواْ ٱقۡتُلُوٓاْ أَبۡنَآءَ ٱلَّذِينَ ءَامَنُواْ مَعَهُ ۥ وَٱسۡتَحۡيُواْ نِسَآءَهُمۡۚ وَمَا ڪَيۡدُ ٱلۡكَـٰفِرِينَ إِلَّا فِى ضَلَـٰلٍ۬

Then, when he brought them the Truth from Us, they said: “Kill the sons of those who believe with him and let their women live”, but the plots of disbelievers are nothing but errors!” [Surah Ghaafir Ayah]

Qatadah, may Allah have mercy upon him, stated: “This is different from the first killing (i.e. previous occasion when the sons of Bani Israel were killed) because Fir’awn did cease from killing, but after Allah sent Prophet Musa, peace and blessings of Allah be upon him, he resumed the killing. [1]

At first, the (killing was aimed at) stopping the emergence of a man like Musa, or an act designed to demoralise Bani Israa’eel and reduce their numbers, or both. As for the second (killing), it was to demoralise this nation so that they would consider Musa, peace be upon him, as a bad omen. [2]

[1] Tafseer Al-Baghawi
[2] Ibn Katheer