The whole ordeal is still going in under some secrecy, but I suspect the main parts that make it controversial are these, from the given article:

• When the inquiry began, it was from an "elastic" understanding of the internal regiment of the Supreme Court. It's a process that, under normal circumstances, requires either a police or the Public Ministry to ask to investigate first.
• In a lone vote against opening the inquiry, judge Marco Aurelio said the process should've begun via the Procuradoria Geral da República
• Everything is still going under secrecy.
• There's no definite end in sight for the investigations

The Brazilian STF has MANY flaws, chief among them of having no "power" that oversees it (the senate does, in theory, but no senator is dumb enough to fight the judiciary), but Moraes is the only son of a bitch with a sprinkle of decency (which I don't expect to last past this "hunt" on the far right) and actually being proactive, unlike every other judge who is a morose sloth that will only react through "notas de repúdio" (notice of disapproval) that nobody gives a single flying fuck about and sit on fucking cases for over a year because there's nobody to tell them to do their fucking job correctly*

Very important to keep in mind is the context. During the entirety of bozonazi's presidency (2019-2022), it was a known "secret" that he used everything he could to incite people against the supreme court. The Gabinete do Ódio (Hate Cabinet), which kept the crazies "informed" with bullshit, was a fact known by everyone. Among said crazies were the fuckers that, in june 2020, fired fireworks at the STF building as a "warning". Bozo and his flunkies threatened the supreme court every fucking week and bozo himself used a meeting with foreign dignitaries to cast doubt on the voting machines. To think all those threats were empty would be pure stupidity, especially when they culminated with the January 8 failed coup.

*Just look at Gilmar Mendes and his famous "perdido de vista" with ADI 4.650, where the old fart sat on the case for 18 months. It wanted to make it illegal for companies and corporations to finance political campaigns. The old fat fuck was in favor of keeping them legal but he knew if the judgement continued, his vote would lose, so he just sat on the case while the 2014 elections rolled with lots and lots of corporate money flowing around.