Does anyone have more information about what the infringements are? It would be very obviously hypocritical for the EU to be publicly alleging "breach of transparency obligations", if they arn't willing to be transparent about the allegations.
Note that they are now starting a formal investigation, whose purpose is to determine whether there are indeed infringements or not.
The EU has broad discretion to start formal inventigations, but specifically CHOSE to begin litigation against X for specific reasons. I would expect a transparent governing body to provide a litany of information to the public about why they are choosing to take that action. If there is a lack of said information, that would lead one to suspect that information is being purposely concealed and/or that it is a targeted partisan political action.
Just to clarify, since I believe "partisan" in the US is often meant to refer to one of the two parties, that the EU has several bodies, and the European Commission specifically consists of people nominated by the member countries and do not necessarily come from the same party (to the limited extent that EU-wide parties even exist).
As an aside, the idea of "disinformation" is fundamentally political/partisan because it defines a grouping of conflicting people and ideas. Furthermore, one of the core principles of liberalism is that people in a society will never be able to agree on "hard questions" (i.e. religion, culture, values, economic system) so the government should not take stances on them. If the EU is a liberal institution, then it is totally contrary to be perusing something as arbitrary and difficult as defining what is and isn't "disinformation". They should be leaving that to individuals and private organizations.
https://euobserver.com/eu-political/136630
The process of selecting the current leader was done in secret.
Even the single-option EU Parliament ballot with her name on it, was a secret ballot.
She replaced the previous leader who is on the record as saying, "Monetary policy is a serious issue. We should discuss this in secret, in the Eurogroup [...] I'm ready to be insulted as being insufficiently democratic, but I want to be serious [...] I am for secret, dark debates."
Then she negotiated massive vaccine purchases from Pfizer that were far too large, and the deal was secret. People wanted to know what sort of negotiation process led to buying hundreds of millions of shots that then had to be destroyed because nobody wanted them, and it turned out she negotiated it via SMS and those messages were ... yep, secret. (in fact, destroyed). This came as no surprise because at the time she got the job she was under investigation in Germany for corruption, but the investigation stalled after phones that were confiscated turned out to have had all their data deleted before being handed over.
The EU insists that almost every website spam you with reams of boilerplate in the name of transparency, but systematically refuses transparency for itself.