Are you referring to the script errors that happen in Internet explorer.
If you are getting that then it is not a fault of IE but a coding error in the web site.
You can suppress the display of this errors by doing the following.
In IE click on tools | Internet options.
then click on the advanced tab.
then check the box "Disable script debugging"
uncheck the box. "Display a notification about every script error"
This should prevent the popping up of alerts in future.
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