Hi Lefteris,
I am sorry for the late replay.
Currently we do not have a support for bundles in out project templates so this behavior is expected. Of course you can manually modify the template. You may find the link below helpful:
http://www.asp.net/mvc/tutorials/mvc-4/bundling-and-minification
Please do not hesitate to contact us again.
Regards,
Vesko
the Telerik team
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