IE 10 is currently not supported by Jira. The lowest supported version of Jira (7.2) lists Internet Explorer 11 as the only supported version of Internet Explorer. Microsoft Edge is supported. See also https://confluence.atlassian.com/adminjiraserver072/supported-platforms-828787550.html
Now in regard to your question to hide the error: that strongly depends on whether this dialog is rendered client-side or server-side. If it is rendered by Jira server-side, it will be difficult to fix this without making changes to the installed instance.
AJS.flag method. You can look at the Jira source code to see when this message is generated and if you can override
AJS.flag in a way that will allow you to hide this message whilst still preserving other notifications.
Keep in mind: if you’re going down this path you might experience a lot of unexpected behaviour and other errors. Without any doubt, the best solution would be for your client to adhere to the supported browsers list.