It's not lens flare and it's not shadow - it's just the limitations of the lens. Of course bumps and knocks can mis-align the elements but in the case of the Canon EF70-300 f/4-5.6 USM IS
it's simply a design flaw, for want of a better description. Once the optics are stretched to their limits they don't perform as well as their L-series counterparts, and softness creeps in. More often than not this softness will emanate from the centre of the frame but it sometimes manifests itself as softness/blur in a particular area, such as the left or right side, or top or bottom of the frame.
Obviously the scale and extent of the softness varies from copy to copy, which is why it's important when buying new to be sure you have the best possible copy. The 100-400L is a serial offender in the softness department, with many people reporting issues right or left side (or both) at 400mm. In the case of the 100-400L there are perfect copies out there if you're willing to play the exchange game (I have one); however with the 70-300 IS
expecting a copy that'll perform brilliantly at 300mm isn't going to happen.