Dixon said Tuesday that she did not "necessarily concede" on election night and is exploring legal options. About 3,000 votes separate Dixon and Pugh, who declared victory based on the unofficial tally.
Dixon had 34 percent of the vote compared to Pugh's 37 percent when early voting and Election Day returns were counted.
The NAACP and community activists have called on Gov. Larry Hogan to request that the state prosecutor investigate Baltimore's Board of Elections, which has been criticized for losing ballots and wrongly turning away some voters on Election Day.
Armstead B.C. Jones Sr., the city's elections director, has dismissed the accusations, saying his staff carried out their duties properly.
A Hogan spokesman said the governor "believes that any election that takes place in Maryland should be completely free of administrative irregularities or fraud of any kind.
"There is a legal and procedural process for issues like this that involves local boards of election and possibly the state prosecutor if the allegations or complaints rise to that level," said Douglass Mayer, the spokesman.
In Dixon's speech on election night, part of which was captured on video, Dixon told supporters gathered at GAME Sports Bar: "If it was God's will, if it was the people's will, we would win. So, it wasn't the will, but we put up a big fight out there."
She congratulated Pugh, but also said, "I'm not through yet."
"If you listen to my remarks, I didn't necessarily concede," Dixon said in an interview Tuesday. "I said that it's not necessarily over."
Jones stressed that the election results are unofficial until all votes are counted.
The city board is processing about 7,000 provisional ballots and more than 3,800 absentee ballots that are arriving by mail daily, Jones said. He expects the final results to be certified Friday. A Maryland State Board of Elections official said that timeline was not unusual.
The board will continue counting the remaining ballots Wednesday morning.
Dixon said that Jones has been inconsistent in the past week when relaying to her campaign the number of ballots yet to be counted.
"He's changing it every day," she said.
On election night, Dixon said, her campaign staff was confused about the results they were getting from city officials.
"Something was missing," she said. "Our folks were watching and counting down to the precinct."
At one point, Dixon said, "we couldn't get some numbers from key red areas," referring to voting precincts that Dixon's camp considered locks to vote in large numbers for the former mayor. Ballots went missing for 24 hours in such areas, she said.
Martha McKenna, Dixon's spokeswoman, told The Baltimore Sun this week that "there are many, many questions about the administration of the election," including a number of polling places that opened late.
Pugh's campaign had no comment Tuesday. Pugh previously told The Sun that she is confident she won and not worried about the election swinging in Dixon's favor as additional ballots are counted.
Todd Eberly, a professor of political science at St. Mary's College, said it's unlikely that the absentee or provisional votes will change the outcome of the election.
"It's really hard to imagine how she closes that," Eberly said of Dixon.
The absentee ballots that have been counted so far increased Pugh's lead, and Eberly said there's no reason to assume that the pattern in the thousands of provisional ballots remaining will be substantially different from the Election Day results.
Dixon's campaign would have three days after the election is certified to request a recount and could ask for every ballot to be counted again or for certain precincts to be checked.
A court challenge must be filed within seven days of a certified result.
State election law gives residents broad latitude to raise questions that elections officials and prosecutors must examine.
Two activists say election "irregularities" raise questions about the city's results.
The Rev. Cortly "C.D." Witherspoon and Hassan Giordano, who have alleged problems during early voting and on Election Day, gathered outside the city's board of elections on Tuesday to call on Hogan to ask the Office of the Maryland State Prosecutor to appoint an independent investigator to examine the administration of Baltimore's election.
The activists are urging any resident who had problems to attend a meeting scheduled for 7 p.m. Thursday at Sharon Baptist Church.
Baltimore elections officials have acknowledged that they could not immediately find eight computer drives of voting results on the night of the primary. Each drive contains the votes for one precinct.
Nikki Charlson, deputy administrator for the state elections board, said the data on the drives is encrypted and cannot be altered. Paper ballots are the official record of a vote, she said.
"I couldn't read it or I couldn't change it," Charlson said of the data on the memory sticks. "I couldn't do anything with it."
Five of the drives were found locked and sealed inside the voting machines the morning after the election, Charlson said. Two others were found in the election office warehouse. The last one has not been located, but officials said they recounted the paper ballots in that precinct.
Some voters have said they were wrongly prevented from casting a ballot on Election Day. Among them is Dixon's sister, Janice, who said she was told she had to vote using a provisional ballot because someone had already voted in her name during early voting.
Giordano, a volunteer with the Dixon campaign, said he has heard from 27 voters who said they had problems. Some errors are to be expected, "but the level of irregularities" in the primary are concerning, he said.
"This by all accounts is at best the messiest election that we've had in the city of Baltimore, and at worst, there is malfeasance and incompetence on the part of the director of the Baltimore city board of elections," Witherspoon said.
Tessa Hill-Aston, president of the Baltimore chapter of the NAACP, said Tuesday she supports an investigation.
"We have worked too hard for voters' rights, ex-offenders' rights and voter registration all over this city," she said.
Activists also were concerned with the outcomes of other city races.
Several candidates who ran for City Council in Northwest Baltimore's 5th District said there were issues with voters from the 5th and 6th Districts being told incorrectly by election officials they were in the wrong location.
Betsy Gardner, who lost the 5th District race by 517 votes, said that during early voting at the Public Safety Training Center on Northern Parkway, "more than a dozen" 6th District residents were given 5th District ballots. She said on several occasions there were not enough ballots. At Langston Hughes Elementary School, there were not pens to fill out paper ballots.
Gardner's supporters told her that 5th District voters were being turned away by confused election workers.
"How many votes did we lose in the 5th District because of the incompetence and lack of training of these election judges?" Gardner asked.
Kinji Scott, another losing 5th District candidate, said he met a woman crying as she was leaving a polling precinct on Northern Parkway because she was told she had already cast a ballot during early voting. She said officials told her to produce identification, which isn't required, and to fill out a provisional ballot.
"There is absolutely no way what happened Tuesday should be allowed to stand," Scott said.
Baltimore Sun reporters Yvonne Wenger, Michael Dresser and Andrea K. McDaniels contributed to this article.