Internal audits relating to appointment procedures suggest some health boards, including NHS Tayside, have massaged their figures.
Other records were not detailed enough to show if patients had been treated unfairly.
Details emerged as opposition politicians said another set of statistics suggest figures were being manipulated across the country until the NHS Lothian waiting list scandal last year.
The Scottish Government published the reports by the 14 health boards yesterday, revealing how appointments are managed in the wake of the Lothian row.
The health board had been accused of fiddling waiting times targets by offering patients treatment at short notice in England.
People who were unable to travel to these appointments were marked "socially unavailable". This enabled the board to delay their treatment without being in breach of the SNP administration's promise to deal with patients within 18 weeks of first seeing their doctor.
In yesterday's reports, Grampian health board revealed patients were marked "unavailable" if they were told they might not be treated within the target time and agreed to a delay.
In Tayside, people were marked unavailable for a range of reasons, including equipment shortages. It stated a number of staff "spoke of instances of inappropriate behaviour including pressure on them to use unavailability to prevent breaches".
And, in certain cases, waiting list managers were "just told to do whatever was required to clear the list" adding that some of this behaviour "could be construed as bullying".
In a sample of records checked by NHS Lanarkshire, 17% of appointments were not handled in line with Government guidelines.
The report notes that "on occasion written offers (of appointments) were being sent to patients two or three days prior to the appointment date".
Health Secretary Alex Neil told MSPs there was "no evidence of deliberate manipulation" of waiting times and maintained the Lothian scandal was a one-off incident.
Mr Neil announced the "socially unavailability" reason for pausing a patient's waiting time had been scrapped. Patients must now confirm that they are unavailable for treatment.
Labour accused Mr Neil of a "whitewash" and pointed to official figures showing a huge fall in the number of patients declared socially unavailable after the Lothian scandal.
A total of 17,360 were deemed unavailable for treatment for social reasons in December 2011. The figure had dropped to 9537 by September 2012.
Large falls were recorded in all mainland health board areas, including a drop from 5693 to 2420 in NHS Greater Glasgow and Clyde.
Health spokeswoman Jackie Baillie said: "We were told by [former Health Secretary] Nicola Sturgeon that it was only NHS Lothian which fiddled waiting times. These reports make clear this was patently untrue. The audits now
show the problems were far more widespread. Across Scotland there has either been deliberate manipulation of records, bullying, retrospective changes to records or records are so incomplete that no final judgment can be made about what has happened.
"Alex Neil's statement was nothing more than a whitewash which failed to recognise the systemic failures. The figures speak for themselves. If there was nothing going on, why has the use of 'social unavailability' fallen dramatically across swathes of the NHS in Scotland since the NHS Lothian scandal broke?"
Mr Neil said: "There is no evidence of deliberate manipulation of the figures like those found at NHS Lothian but there are improvements in waiting times management that can be put in place."
Norman Provan, associate director of the Royal College of Nursing, said: "The fact that all health boards have now published and made publicly available their individual reports on waiting times means that any specific local issues and recommendations can be considered in a transparent and open way."