In some instances the size of the loan increased on each occasion - with the highest loan being as much as 23 per cent of the fund's assets.
In addition, some funds did not have investments in the name of the trustee and not all appointed all fund members as trustees or directors.
People have breaches because they are trying to manage the funds themselves in a complex area of law, Partners director Martin Murden said.
"The vast majority who had problems didn't realise it," he said.
"People are trying to do it [themselves] and you just can't keep up with it all the complexity."
Murden said an inability to separate the fund's assets from personal assets raises questions about the security of fund investments and where dividends were going.
"What often happened was that dividends paid by cheque to fund members were being deposited into personal bank accounts and similarly, if shares were sold, these payments were not automatically made to the trustee.
"This is an absolute no no," he said.
SMSFs are the fastest growing area of super behind industry funds. The Australian Taxation Office recently tripled its SMSF compliance officers from 140 to 500.
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