Stay at the same place to plant the seed just click different place in front of you. Sometime other seed already plant few seconds before disappear.
Same behavior in beta 10.
More detail to reproduce: This happen in a zone the light is not enough powerful. (More that 4 or 5 squares of a torch in a cave)
This could be the normal behavior but not intuitive.
If you plant just one seed in this dark zone and wait, you see the seed popup after may by 15 seconds.
Crops require a light level of at least 9 from blocks, or to be exposed to the sky.