Can you please provide us screenshot of those special characters in both JIRA and Salesforce.com? Can you please let us know if those value in comment or field?
Can you please provide us with the debug log of the Connector. We need the debug log for the Connector in order for us to investigate further on this issue. (If you're using JIRA Cloud/On-demand, please send a request to Atlassian Support to enable and retrieve the log for the Connector)