Please use the Editor.DisableClassList Property to disable the classes which cause the problems.

Example:

DisableClassList="Toobig, TooWide, Useless,...."

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Another solution is you can set Editor.AutoParseClasses Property to false. Then add your own CSS Classes using the following methods:

1: Edit Dropdown Configuration file (Common.config).

The dropdown configuration file (Common.config) can be found in the /CuteEditor/Configuration/Shared folder. In dropdown configuration file you can find the CssClass element which contains the configuration information for the CSS Class dropdown within Cute Editor. 

2: Programmatically populate the CSS Class dropdown

Please check CSS Class dropdown Customization for details.