is there something wrong with my new board? 

Been handling it and now it feels like splinters are in my hands, too small to see but they hurt if I create friction. This is a nitro fate,  brand new. I live in Australia and bought it onlinefrom America.

Do I just need to run a cloth over the board and give it a clean or is the top sheet/base compromised?

Welcome to Boardworld, grapnumderpa.

I would think that these are just loose fibres that are still on the board for whatever reason. Definitely give it a good wipe down with a wet cloth.

Worth noting: this is one of the issues with buying from overseas. If there was actually something wrong with the board, you would not be covered by warranty in Australia.

yep sure sounds like fibreglass splinters to me.  I would wipe it down with several rags then throw the rags in the bin.