Among the reasons the deals were suspicious was that they were high-volume trades involving companies that showed little or no business activity, at a time the companies were being heavily promoted.
The company's trading surveillance system was flawed during the time in question, but even in cases where the system raised red flags on transactions, employees responsible for acting on the information failed to file the required reports, according to the SEC.
Finra also noted that Aegis failed to file SARs despite being alerted to the suspicious activity by its clearing firm.
Eide was cited by the SEC as having caused the violations by ignoring warnings about the trades.
"Throughout the relevant period, Eide was alerted to at least some of these suspicious low-priced securities transactions as well, but he failed to take adequate steps to ensure that Aegis was filing the requisite SARs," the SEC said in a filing.
Kevin McKenna, formerly Aegis Capital's AML compliance officer, was found to have "aided and abetted" the firm's violations and agreed to pay a $20,000 fine. Under the agreement, he is prohibited from serving in a compliance or anti-money-laundering capacity in the securities industry, with a right to reapply, the SEC said.
Under the agreements, Eide and McKenna neither admitted nor denied the SEC allegations.
A third employee, Eugene Terracciano, a former Aegis Capital compliance officer, has been accused by the SEC of failing to file SARs on behalf of the company. His case is scheduled for an upcoming administrative hearing, according to the SEC.