The reason for that is that the Parliament was trying to reject a law the Council had already agreed on.

The EU legislative process (ordinary legislative procedure) works like this: Parliament and Council take turns on a bill. Once the Council has adopted its position and it comes back to Parliament for a second reading, the default flips. The bill passes automatically unless Parliament actively rejects or amends it. And rejecting at second reading requires an absolute majority of all 720 MEPs (361 votes), not a majority of those voting.