Perhaps the most consequential decision that special counsel Robert S. Mueller III included in his 400-plus-page report on Russian interference in the 2016 presidential election was that it wasn’t his place to decide whether Donald Trump obstructed justice.

But as we continue to learn in the weeks since the report dropped, intriguing stones were left unturned in other areas.

The release of a voice mail from Trump lawyer John Dowd to a lawyer for former national security adviser Michael T. Flynn has reignited questions about how far Mueller did and didn’t go in his investigation. In the voice mail, Dowd probes Flynn’s counsel for tips about what Flynn might share with Mueller’s team after cutting a deal. Dowd also alludes to Trump’s warm feelings about Flynn — which, when heard in the actual audio, carries clear overtones of a potential pardon.

Elsewhere in the voice mail, Dowd tells Flynn lawyer Robert Kelner that if anything Flynn says “implicates the president, then we’ve got a national security issue, or . . . some issue . . . not only for the president but for the country.” He adds that, even if Flynn’s team can’t share anything, “remember what we’ve always said about the president and his feelings toward Flynn, and that still remains.”

As Michael S. Schmidt and Charlie Savage analyzed this weekend for the New York Times, the voice mail would seem to present a compelling avenue of inquiry for Mueller — especially if it delivered a message that Trump himself authorized. The voice mail could have figured into the obstruction investigation, and some have argued that it sounds a lot like witness tampering. It’s somewhat similar to other potentially obstructive episodes Mueller detailed in depth — most notably, Trump’s conduct toward former campaign chairman Paul Manafort, which included publicly leaving open the possibility of a pardon.

Mueller’s report says his team did not interview Dowd “because of attorney-client privilege issues.” As some legal experts have noted, though, that privilege doesn’t extend to illegal conduct. So if Mueller believed this voice mail might be part of illegal acts, he could have fought to get the interview.

But this isn’t the only interview he could have sought that seemed to have some bearing on questionable — and potentially illegal — conduct. There is, of course, the big one: an interview with Trump himself. Despite obstruction charges requiring evidence that the alleged perpetrator intended to obstruct legal proceedings, Mueller relied only on written answers from Trump and other evidence to establish his frame of mind. His report indicates that, even though he regarded Trump’s written responses as “inadequate,” he decided that a protracted subpoena fight over an interview with Trump would have delayed the report too long.

Mueller didn’t interview Trump’s eldest son, Donald Trump Jr., either, even though Trump Jr. organized a Trump Tower meeting with a Russian lawyer pitching dirt about Hillary Clinton. Mueller said that he considered charges against Trump Jr. but that he didn’t believe the government could prove he acted “willfully.” An interview with him probably would have shed some light on that topic. The Mueller report says Trump Jr. declined to be interviewed, but again, Mueller could have fought for the interview.

Mueller’s report also doesn’t dwell upon several other key elements here. It devotes little space, for example, to questions about the president’s finances, including his business ties to Russia or other foreign governments — a hole Democrats have said they intend to fill in the course of their investigations. The omission is particularly striking given reporting that suggested Mueller was probing these areas, crossing Trump’s self-declared “red line” in the process.

Nor did the report delve far into key allegations made in the much-discussed “Steele dossier.” For example, it only briefly mentions the dossier’s claim that Michael Cohen, a former Trump lawyer, traveled to Prague to strategize with Russians in the summer of 2016. And rather than lay out evidence, it merely states that Cohen himself denied it, without indicating whether that claim stood up to scrutiny.

“Why didn’t Mueller finish?” Senate Intelligence Committee Vice Chairman Mark R. Warner (D-Va.) said last month, according to the Bulwark website. “There’s great controversy around the Steele dossier, and, I mean, I think it was glancingly mentioned at best. And I’d like to know. They had a lot more resources than we — I think that’s an important issue for the American people.”

Conducting an inquiry of the size and scope of Mueller’s and then summarizing all of it, even at more than 400 pages, is liable to leave plenty of people disappointed about what was not investigated or said. But these exclusions are certainly some of the more conspicuous ones, and they suggest, at the least, that Mueller wasn’t some prosecutor hellbent on taking Trump down at whatever cost, as Trump has argued.

They also suggest that there is still plenty more that we don’t know — and may never know.