Carolyn Leckie was speaking at the trial of Natalie McGarry, who is accused of misappropriating more than £25,000 from two campaign groups.
The 40-year-old, who was MP for Glasgow East between 2015 and 2017, is charged with embezzling £21,000 while she was treasurer of Women for Independence (WFI).
A second charge accuses her of embezzling £4,661.02 from the Glasgow Regional Association of the SNP between April 9, 2014 and August 10 2015.
The 40-year-old denies both charges.
Ms Leckie, a former Scottish Socialist Party MSP gave evidence at the trial on Wednesday after it was adjourned for two days due to McGarry being unwell.
During the hearing, Allan Macleod, defending, presented to her and the 14-strong jury multiple cheque stubs showing various amounts paid from the WFI account.
One cheque included the sum of £700 to be paid as wages for Kathleen Caskie and Kezia Kinder, two WFI members who were employed by the organisation.
When the defence asked how one cheque would be able to pay for both employees, Ms Leckie said: “I suspect it was cash payments, but I don’t know.”
The court heard a standing order was set up for wages which was “ongoing” after Ms Kinder’s employment with the group ended.
Mr Macleod added: “So essentially, was she (Kinder) paid her wages after leaving by mistake? Does this tell you the finances were ran in a haphazard way?” to which Ms Leckie said: “Clearly there were issues.”
Other cheques shown in court included one for postage on 22 January with no year date or amount written on it.
Another undated one addressed to the organisation Positive Prisoners was shown with no written amount.
It has been alleged McGarry cashed cheques held in the name of WFI while managing the group’s finances and transferred money made from fundraising events into her personal accounts.
The court heard McGarry told Ms Leckie and former health secretary Jeane Freeman, who was also a co-founder of the campaign group, that she was “more than prepared to pay what you see as the outstanding balance until it is proved undoubtedly that the money was paid out, at which point it can be reimbursed.”
Citing an email from Ms Freeman, Mr Macleod said: “Certainly so far as Jeane Freeman is concerned, that appeared to be an acceptable agreement.”
But Ms Leckie disagreed, saying: “No, I don’t think she found it acceptable because of the history of trying to get the information.
“I think there was a point where we felt that if this was about disorganisation, if it was a muddle not a fiddle, that would be appropriate to let her pay it back.
“But increasing concerns were growing in Elizabeth’s work that there was something more sensitive and we were not prepared to establish that and we didn’t want to be in a position where we were covering up potential criminality.
“If Natalie can explain now that there’s no criminality, that’s the job for the police, for the Crown.”
The trial, before Sheriff Tom Hughes, continues.