SGVO do conduct spontaneous check on the accuracy of documents received, however this is rare and very unusual. Unless they have some huge suspicions over your provided documents, chances are that your files are randomly selected for fraud checks. I see that you are from Singapore too, I personally feel that if you have provided true copies of your employment certificate, there shouldn't be any concern.
'the concern is that the submitted references are not official i.e. they were not issued by company officials or under the company's authority at time of issuance. That is the misrepresentation of concern.' I feel that this statement spells trouble, though I may be wrong. Could you provide another employment certificate and possibly a name card of your reporting supervisor for further verification? Please be reminded that misrepresentation can constitute to having your visa rejected for at least 3 years. Rather than having your application repatriated, please do the necessary explanation cautiously.
Hope this helps.