Ms Swinson's campaign spending came in £210 below the legal limit, but reports say this was only after almost £7,000 of costs were disregarded.
The SNP said there were "serious questions", with the Lib Dems "living dangerously close to spending limits".
The Lib Dems said they had complied with all Electoral Commission rules.
Ms Swinson re-took the seat from John Nicolson by a margin of 5,339, a 10% majority, having previously lost out to the SNP politician in 2015. She was subsequently made her party's deputy leader.
Her official declaration of expenses was within legal limits, but only after £2,700 of leaflets and other material bought by the party went undelivered - thus not counting towards the total.
A further £4,040 of costs were registered as "national" spending, promoting the party generally rather than Ms Swinson's local campaign.
The SNP said voters would "find it hard to believe that so much cash could be spent on leaflets that just vanished", adding that: "It was an election, not an illusion show."
A spokesman said: "These revelations raise serious questions over the Lib Dems' campaign in East Dunbartonshire. People have a right to know what has gone on here. They have been living dangerously close to spending limits - and seemingly writing off thousands in costs to keep them within the rules."
However, a spokesman for the Scottish Lib Dems said all spending was above board, and said the SNP were "smarting" after losing 21 seats in the elections.
He said: "All Liberal Democrat candidates follow the clear guidance they are given about election spending, and our party's compliance team are in constant dialogue with the Electoral Commission to ensure that we are abreast of the latest advice and abide fully by all their requirements.
"All expenditure in this election was apportioned correctly and clearly identified in our election return which is now a matter of public record.
"It's understandable that the SNP are smarting from a disappointing result, but they should accept that they were beaten in a fair fight in seats right across Scotland, and concentrate instead on the important business of running the country."

The airline did not operate 331 flights after cancelling 248 on Wednesday.
Some passengers have been stranded in European cities after Easter breaks, prompting Easyjet to operate five "rescue" flights on Friday.
The flights will bring three parties of schoolchildren back to the UK.
The additional flights will run from Luton to Paris, Paris to Barcelona, Barcelona to Luton, Gatwick to Madrid, and Marrakech to Gatwick.
Easyjet says it will put larger aircraft on routes that have been most affected to allow more passengers to get home.
A spokesman said the "unnecessary" strike had caused "considerable and disproportionate disruption for passengers and airlines across Europe".
Rival low-cost airline Ryanair said it had been forced to cancel more than 500 flights over the last two days.
"We again call on the EU [European Union] and French authorities to act now and prevent  thousands of travellers being held to ransom by these French [air traffic control] workers," the Irish airline said.
Johanna Booth, from Liverpool, has been stuck in Barcelona after two Ryanair flights were cancelled due to the industrial action.
"We have a four-month-old baby and his formula milk has ran out and he is not drinking much of the other variety, so I am concerned," she told the BBC.
"The support we have received from Ryanair has been minimal."
Air France said it was operating one-in-four flights to and from Orly airport in Paris, about 40% to and from cities in the rest of France, and 50% of medium-haul flights to and from Paris-Charles de Gaulle airport.
No long-haul Air France flights were affected on Thursday.
Air traffic controllers are planning further industrial action from 16 to 18 April and from 29 April to 2 May 2 - both key holiday periods.
Roger Rousseau, head of the SNCTA union that represents French air traffic controllers, said: "We can assure our passengers that we are doing everything possible to limit the inconvenience of this strike on them."
Among the issues upsetting members is that the retirement age will be raised from 57 to 59.
Questions have been raised over the general election expenses of Liberal Democrat deputy leader Jo Swinson in East Dunbartonshire.
[NEXT_CONCEPT]
Easyjet has cancelled hundreds of flights as the second day of strike action by French air traffic controllers took its toll.