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Just rebuilt CRF250R 2016, after riding for a couple of hours every thing seemed to be going ok just a bit of popping when slowly down, oil and water levels full. Jumped back on and didn’t have first gear, had a play and could only get 2nd and 3rd so decided to take case off and soon seen it’s smashed the water pump gear? All fluids where still full and engine still runs. Still investigating but any direction would be greatly appreciate.

Welcome to the site !!

A little confused on your questions ........ You said you rebuilt the engine and had no gears .... so the clutch ?? or the tranny ??? , went bad (no oil ??) ...................... Then you mentioned the water pump gear being smashed ..... I am totally confused as to what is going on here ..... need more info than a 1 paragraph explanation .... , the more details you give , the easier it is to diagnose ....

Yep a better explanation of what is wrong and photos would help.
Did you replace waterpump or its bearings during the rebuild.
Was the oil still full when everything stopped working?

Is the gearbox smashed up or just loss of gears as in can't select?