Having taken a closer look, there's nothing really nefarious going on: what is mainly happening is that every step of the very long process of passing a EU regulation is getting lots of attention.

Back in 2020 or so the commission first proposed the reform that contains the chat control provisions, then there was like a year or two of well published fighting in the European Parliament (EP) before they reached a position on the entire reform (notably excluding chat control).

Meanwhile the council of minister (effectively the upper house of the EP) didn't get around to forming an opinion before the parliament, so they are doing that now, which means it the same fight over chat control all over again but with different people.

After the council of ministers agrees on a position on the entire reform proposal from the commission we'll get even more rounds of bickering over what the final text should be: the trialogue. Those tend to be very closed, but with how much attention chat control is getting expect lots of leaks and constant news about who's being an ass during that step too.

Note that it is explicitly expected that each of the thee bodies will come up with different positions on many aspects of a regulation proposal, so there is nothing strange with the commission or the council suggesting some the parliament has opposed.