This bug first and also reported on GitHub. I have also noticed another error that could benefit by a fix to this bug (GitHub: Generic icons which aren't an application appearing in dock #136). The bug is the title: Programs started that have rules created for them should be respected, whether those rules are user or system created. This could pose a security risk. If mate-dock-applet respected or searched against/validated its current running apps against the tasklist, it could narrow down or eliminate errors. To save resources this check would only have to be performed when the applet adds a new window.
I noticed this bug because I have some programs and scripts that start-up hidden from certain users (kids/students) to log and prevent user attempts to backdoor security measures (i.e. you cant type or copy to the clipboard the word 'proxy' or 'firewall' without the word(s) being replaced by the name of the user). For me, this applet is useful and I would like to make it available to other users, but this bug presents a security risk by not respecting those settings.
I have not elevated this to a security bug on launch pad, because I believe I have a special use case. However, if this bug could potentially lead to exposing/misidentify system programs that should remain hidden and revealing them to the user or granting a user elevated control when they shouldn't, then it poses an obvious and dangerous security risk. I welcome any admin to elevate this bug to a security risk if they believe my 'special use case' simply revealed a glaring security bug.
It is possible to have the programs launch asynchronously with a script using devilspie. If webkit (or some other library) is what you have to use to make this applet work, perhaps there is a command I can send to the service that provides that information to the applet to ignore or delist certain windows as a work around?