Sounds like your hub gears are slipping, your chain is not engaging properly (too much slack? too much torque?), or some combination thereof.

Do you ride in inclement weather? Moisture intrusion into the hub and/or chain could be causing a lot of these issues.

It is also possible that the hub was defective and only revealed itself after a certain amount of riding, or the cable shifter into the hub slackened and you got caught between gears.

Maybe a couple ideas here. First, if you ride in inclement weather, dry your bike thoroughly after each ride and re-oil the chain periodically. Second, you're aiming for smoothness on the pedals, not brute force - so if you hammer down on the pedals in a really high gear, might be causing some drivetrain slippage.

I'd hate to see you get turned off by this bike, but it's unclear exactly what is causing your issues.