They are looking into the same thing they got Manafort and Flynn for, working as a foreign agent without registering as such.

I know that previously Podesta group did some lobbying where they didn't register under FARA but registered with Congress. There was a question they if that was legit or loophole or straight up illegal.

Since NBC called them a "subject" of an investigation that means Mueller is not just seeking information that can be used against Manafort. That would be a witness. A "target" of an investigation is almost surely to be indicated. Manafort is likely, officially a target since they got a search warrant against him and searched his house with no warning. The NBC article says

The sources said the investigation into Podesta and his company began as more of a fact-finding mission about the ECMU and Manafort's role in the campaign, but has now morphed into a criminal inquiry into whether the firm violated the Foreign Agents Registration Act, known as FARA.

A subject may end up as a target.

If you are involved in a federal investigation, one of the things that will be of incredible importance to you is your status in the investigation. There are three statuses, let me talk about each of them.

The first status you have to worry about is being a target. A target is the person to the prosecutor is gunning for, that's the target of investigation. It's the person who the prosecutor believes has committed a crime and their trying to figure out what the crime was and how to build a case against them.

A witness, on the other hand, is somebody who has really got very little exposure. The prosecutor believes that the person hasn't done it wrong, they simply have information, they were there, they saw something, they have documents that relate to something. They're not caught up in it.

The last status is in-between the two, you’re a subject. **And so if you're subject in an investigation what that means is that you're not a target, so they're not gunning for you, but the prosecutor thinks that there is good reason to believe you may have done something wrong. **You may have committed a crime or been a part of a criminal activity or part of a conspiracy.

https://www.whitecollarcrimeresources.com/targets-subjects-and-witnesses-in-federal-investigations.html

When a person is a “subject” in an investigation and called to testify before the grand jury, the prosecutor will advise the person of the following rights:

The grand jury is conducting an investigation of possible violations of federal criminal laws. The subject may refuse to answer any question if a truthful answer to the question would tend to incriminate the person. Anything the subject says may be used against him by the grand jury or in a subsequent legal proceeding. If the subject has retained counsel, the grand jury will permit him/her a reasonable opportunity to step outside the grand jury room to consult with counsel if necessary. If the person is a target in the investigation and is going to provide testimony before the grand jury, then the prosecutor will supplement the preceding rights with the following target warning: “your conduct is being investigated for possible violation of federal criminal law” (or words to that effect). https://www.lexology.com/library/detail.aspx?g=d70e9881-c7e0-4ac8-82d5-650de9b98fc9