20 minutes is not very long for numb anything to set in, make sure your glove straps aren’t so tight as to limit circulation 
coming from a cruiser sportbike riding position would feel very unnatural so you might be placing very little weight on the legs and transferring way too much weight on the bars and on your privates. In a normal riding position I can lift both hands from the bars without pushing off or shifting any body weight to compensate. I do alternate between an arched and curved spine posture on long rides, that reduces muscle fatigue and numb bum.
Ninja 250 being a parallel twin she will have some engine buzz, someone else can tell us if the stock bars are rubber mounted as they are on many other bikes. It does have a chain and chains transfer an amazing amount of vibration through the whole motorcycle, especially if they are not adjusted correctly. Shame on the dealer if that was the problem.
Gloves can make a world of difference, if you weren’t wearing any that could be a problem, gloves are almost as vital as a helmet. Personally, I like gloves with a single layer of leather on the palm, any built up layers or insulating material on the palm is not so good, can result in calluses or hand cramps, don’t like the padded grips either.
Control lever positioning can make a big difference, just as keyboarding wrong can give you carpal tunnel.
…hope this helps some
