That is the whole point of the illusion, that there are two filled circles that flash and your brain perceives it as 3 flashes because they come so fast that they are processed as a temporal chunk before you become aware of it.
Look at the explanatory diagram with the labels "What our eyes see" and "What our brain "sees"" (the third image on the page).
The gif is just broken. It's supposed to have a space between the second and third flashes.
Where is this from?
I could be missing something, but everything I can see in the article and the abstract of the paper indicates that the point of the illusion is that showing three flashes causes us to misplace the second flash as being located at the midpoint of the first and second.