OK - you mentioned 'lens cap' rather than hood - the lens cap I'm assuming is an error, as that can easily be kept out of the shot (if yours is hanging on a leash or something, simply take it off or hold it as you shoot). You mentioned you're not using the lens hood, so that issue should be OK - the lens hood will often get in a shot when you use a flash, so always make sure you take it off, which it sounds like you do. The last choice is that you may have a lens that gets caught in the built-in flash of the camera - this is often when the lens is longer than the kit lens, or if the focal length is significantly wider - the solution is to not use the built-in flash with this lens, buy a hot shoe flash which sits up much higher on the camera body, or use something to 'bounce' the built-in flash up away from the subject - which can be done with homemade pieces of paper, plastic, foil, etc. If you're shooting subjects very close like this, the built in flash is a poor tool - either use higher ISOs and/or a tripod and no flash at all, or use an external hotshoe flash. Just a few ideas.