Small red squares indicate that Dragon can not decide if that intersection is black or white territory. Possible reasons are:

• Inside a territory there are still foreign stones which have not been marked as "dead" yet. Please click on those stones to toggle the status to "dead".
• The borders of White's or Black's territory have not been closed. For human players it is obvious, but for Dragon it is difficult to decide who owns which territory. Please click on the "resume playing" link below the board and submit a move to close that border.
• It is a seki position. Please click on that red square to toggle it into a dame. Dragon will visualize it with a small green square. This feature allows you to resolve a doubtful seki to a correct game result.
  In other words, if you see a green square, it is a dame.