The dark blotches are often associated with a fungal canker disease, though occasionally it might be due to stress from environmental conditions like weather. It may not matter too much in this case since most of them will be pruned off, since shrub roses like Knock Out varieties are pruned back fairly far each winter to refresh the plant. The exact height varies, but they tend to be cut down to about 15 to 18 inches off of the ground. (A mature, healthy shrub rose will flower normally and reach its full height - potentially 5 feet tall for Knock Out roses - even if cut back this drastically every year.) The time to prune is right about now, in the window of time from late February through mid-March or so. It can be done later into spring, but might delay the start of blooming at that point.

If any canes (stems) are fully darkened and look shriveled and drier, they may have died and can be cut back to wherever they connect to live wood. You can also wait to see if any canes leaf-out weakly or not at all and then prune those off at that point, when it's easier to see how they're growing compared to healthy, vigorous canes.

Miri