Chances are, they are right.
Before you jump to the conclusion that they are "wrongly filtering", I would suggest you audit your site to make sure everything really is in order. You should review the generated output of your site as served up not to you but to an anonymous user on the internet (use a proxy server to reach it from something other than your known address and an incognito mode so you don't send the site cookies etc).
It's quite possible your server is infected with some kind of malware that does inject dangerous objects in your site as it is served. It is also possible you just have some programming mistakes that are potentially dangerous. You might not be properly signing a java applet, you might be serving up something cross-domain, you might have a dangerous javascript hack in your code, or any other combination of trigger factors.