Here's my understanding of the alleged issue
Following the brexit vote in 2016 Nicola announced in 2017 that an indyref2 campaign was being launched. The SNP then started an online fund raising exercise promising to spend every penny raised on independence campaigning. Between 2017 and 2021 they raised £667,000 but it then became apparent when they published their accounts that most of that money had been spent (obviously not on an indyref2 campaign given there has been no indyref2).
in July 2021 police received 7 complaints from SNP members that a fraud had taken place as the money was spent on items other than what it was raised for and they opened an investigation. I can only presume that this investigation turned up sufficient evidence that resulted in Mr Murrel's arrest yesterday. There is no information that I can see in the public domain that suggests whether the allegation is that the money was spent on general SNP business or spent on other items.
Separately Mr Murrell loaned the SNP in 2021 £100K to address a short term funding shortfall in respect of general SNP spend following the 2021 election. I seem to recall reading somewhere that some of that loan had been repaid subsequently but not all of it.
One might speculate that all of this seems like the symptom of a party spending beyond it's means