This turn button thing could be the result of the game waiting for you to tell your ships where to go. Depending on what you set for autopilot in the game's options, when an autopilot ship is sitting out in space with moves left, or if one is on guard or sentry duty and 'sees' another ship, it will wait for a response from you. The turn button not showing up is a way of notifying you of this.
So next time this happens:
Press the 'Tab' key to cycle through the ships/fleets that are 'waiting for orders'
Press the 'Space Bar' if you don't want to give orders to whatever ship/fleet is selected.
Once all the waiting ships have been given orders, the turn button should become available.
There are other things that will cause problems with the turn button, but I think those are bugs, so if what I described isn't relevant to your issue, email [email protected]
If what I've said above is what you are experiencing, and you find it annoying, you can disable this behavior by going into the Game Options screen and enable the option 'Skip Moves Left Over From Auto Pilot'