remove black frames from vob files with ffmpeg
What you experienced are called dropped frames.  These shouldn't be confused with drop frame video formats (such as 29.97fps NTSC video, which is otherwise known as 30 fps drop frame (because a frame is dropped to get 29.97 frames per second.) 

Dropped frames occur when the system capturing is not able to keep up with the rate of playback.  They are duration .04 because it is a single frame, which works out to around .04 seconds.

Dropped frames are a relatively tricky issue to deal with as they interfere with the flow of the video and also the audio sync.  Even if you clip them out of the source material, it results in a spatial and auditory gap of .04 seconds that is often detectable by a viewer.  Due to this, the best practice is to re-capture if you experience dropped frames during capture.

If re-capture isn't an option, your best bet is to interpolate a frame to fill the gap by averaging the preceding and proceeding frames of video.  This frame often doesn't come out super well, but it is still often less jarring than removing the frame entirely and allows the audio to continue normally (provided the audio didn't also cutout for the dropped frame).

As a last resort, you can simply cut out the dropped frame, but as previously mentioned, this results in a .04 second gap in your footage and is non-ideal.