If you look very closely at your full size image on Flickr you may agree with me that the inner area of the top of the flower, the brown grainy area you can barely see between the extended parts the bee is sitting on, appears to be sharply in focus, as do the tips of some of the yellow/orange parts (whatever they're called) just in front of the bee. There are a couple of possibilities - the image is sharp where you focused, as it should be, and the very limited depth of field is making you think you missed focus because so little of the image is in focus, or you have a front- or back-focusing issue where you focused the camera on one area but the actual area in focus is in front of or behind the point of focus according to the viewfinder because the camera and lens are not working together perfectly during the focusing process. Even if the camera and lens are working perfectly, with the very narrow depth of field shooting this close at f/1.8, it will be very difficult to get good focus on exactly what you want unless you're very careful, preferably by using a tripod and possibly by using Live View focus, if available on your camera. For example, if not using a tripod, even if you focus perfectly if you rock your body backward or forward even a fraction of an inch before pressing the shutter you will throw off what's in perfect focus in the image because of the very narrow depth of field. You can test for front/back focus by setting up a row of AA batteries on a table top and shooting them at a 45 degree angle, with focus on the middle battery and aperture at f/1.8. If possible, use a tripod, and do the test either outside in bright light with a fast shutter speed or inside using flash. If the camera is front-focusing the middle battery, which should be sharply in focus, will be out of focus and a battery more toward the front of the row will be in focus; if the camera is back-focusing the sharper batter will be behind the middle battery.
You can get more information on depth of field here:
http://www.dofmaster.com/dofjs.html
Depth of field is generally defined as the area of the image in "acceptable" focus. Assuming you're shooting with a "crop sensor" camera, at 50mm focal length and f/1.8 and a shooting distance of three feet, your depth of field would be about .84 inch; shooting from two feet, it would be about .36 inch.