I recently started to have problems shifting which turned out to be a frayed cable inside the shifter that would occasionally catch. Carefully inspect your shift cable, especially inside the shifter. Consider replacing the cable even if it doesn't show any wear. (I replace mine every year and the cable housings every 2 years just as a routine maintenance thing. Do-it-yourselfers can replace both shifter and brake cables and housings for about $30.00 total).
If your problem turns out to be unrelated to cable issues, you may just have a crapped-out shifter. Unfortunately, Shimano shifters are not rebuildable. There was a time about 5 years ago when Ultegra 9-speed right shifters were somewhat notorious for crapping out. I think their warranty is 2 years--you might qualify for a free replacement.
Worse case scenario, you'll have to replace the one shifter on your dime, which should cost between $100and $200.