It's hard to say what's going on in your project without seeing the file, but I suspect there's a conflict occurring between your Smart Bone Action and manual keyframing. In other words, I believe this is not a bug but a rigging and animation workflow issue. The trick is to include the ability to add animation offsets fo the rig.
To demonstrate, I reproduced your character but applied my offset items, and I'm able to add my own animation keys on top of the Smart Bone Action keys. Like so...
Here's another example using a tilt control...
What I've done here is I added an extra 'face' bone called faceA, which the headTurn and headTilt Smart bones move side-to-side and up-and-down, respectively. Then, after setting the keys with the Smart Bone, I hand animate the face bone parented to faceA to move the face...this is my face 'offset' bone. Since the Smart Bone does not control this bone, I can animate it freely and avoid any potential Smart Bone conflicts.
In this rig, the faceA bone is located directly under the face bone (it's the green bone in the image below.). After animating this bone for the Smart Bone Actions, I will Shy it so I don't accidentally hand-keyframe it in the Mainline when I meant to animate the offset bone instead.
Note that the faceA bone is being controlled by two separate Smart Bones...so why don't these conflict with each other? It's because the turn bone only controls the horizontal motion and the tilt bone controls only the vertical motion.
To animate the position and rotation of each eye independently of the Smart Bones, I hand-keyframe the bones for these items directly. Because these bones are not controlled by the Smart Bones either, there is no conflict.
Another way to avoid Smart Bone conflicts is to place your art inside another group, have your Smart Bone control that group, and then do your additive keyframes to the child group. In this case, the child group is your 'offset' group.
Actually, there are many ways to avoid conflicts, and the best approach depends on your character design and how you wish to animate it. The key is to avoid situations where keyframes are fighting for control over the same item.
The above ideas should give you a good framework for figuring out the offset items that will work best for your character. Hope this helps, and good luck!