If you are using back-button focus (that is, pressing "AF-ON" (for Canon cameras) or a similar button on the back of the camera, instead of half-pressing the shutter before taking the picture) the camera will record focus information in this way: the focus point will be pre-selected, because you pressed AF-ON (or a similar button) for measuring and locking the focus. However, the camera will not record this focus point as "used". The reason for this is that in the second or so when you moved your hand from the AF-ON button to the shutter button, the subject might have moved or the scene might have changed in other ways. Thus, at the moment when you finally pressed the shutter, the camera has no way of knowing whether your subject was indeed in focus or not, and prefers to record this as "autofocus not acquired". (Compare this with the "normal" mode of acquiring focus, which is to focus upon half-pressing the shutter and then pressing the shutter - it all happens in the same moment, so the autofocus is guaranteed to be "current".)

For all practical purposes, this is usually not a problem - you will most likely not have used back-button focus with a rapidly moving subject, and thus will know that the subject is in focus anyhow. But the camera (and the plugin) will report it differently, which is correct from the camera's point of view.

Note that if you are using back-button focus, there is the alternative to keep the AF-ON (or similar) button pressed until (while) pressing the shutter. This way the focus point will be recorded as both "selected" and "used".