I keep having instances where I show to have a fleet at coordinates but when you click on the fleet there is no fleet there. http://prntscr.com/lm98wc
this is just one of many time this has occurred. sometimes I see alliance members or friends at coordinates as well but when I click they are not actually there.

    
Tried clearing cache and refreshing browser, also opened game in a different browser all together and still get these fleet icons  

http://prntscr.com/lm9iwe     http://prntscr.com/lm9jaa   http://prntscr.com/lm9qgx
http://prntscr.com/lm9r9c   http://prntscr.com/lm9reu   http://prntscr.com/lm9uhr

I have noticed that sometimes after a while they just disappear and will reappear maybe the same coordinates and maybe different ones, but always at coordinates that I have not moved my fleet to.
Also for the enemy screenshots one of those were real and was a scourge that I should not have been able to see. he was not in motion and it was not blinking, but I could clearly see it only when I clicked it showed nothing. but when I flew to the coordinates it was indeed a scourge there.

seeing the same thing periodically. fleet looks like its there but nothing is.  http://prntscr.com/lma8he  http://prntscr.com/lmaek3

 
Partially done. All new cases please describe here.

Whatever you guys are doing has helped.
Though I do still see them at times usually after moving from one coordinate to another in the same system of planets; I have noticed that refreshing the browser or clearing the cache usually fixes it now. The ones that disappear are from my own fleet that was at those coordinates but then had been sent to a new coordinate. After the fleet arrives at the new coordinate the phantom fleet still shows at old coordinate (sometimes still blinking) however after a browser refresh they usually disappear.


  

I also found that on the Phantom Fleets where refreshing the browser gets rid of them that zooming way out and back in will also cause them to disappear

[http://prntscr.com/lqqveu]  [http://prntscr.com/lqqvs0]
after browser refresh they disappear [http://prntscr.com/lqqw8w]

PlayDragon, 
Obviously you are playing in multiple tabs of the same browser or different browsers. I have noticed that the galaxy page is not updating when on the background, all the times. Especially when I have more than one galaxy pages open.

This may cause phantom fleets to be seen where those have already departed. Page refresh is the safest solution to that.

If devs force page update in the background, they endanger to make it unusable due to excessive load on CPU/GPU.

Snoopy
This could be the case now as I do play in multiple tabs, however I have played in multiple tabs
the entire time I have played this game and up until a few weeks ago I had never seen this occur.
It all started around the time of the updates to fleet waiting for warm up before flying. Now I am
not saying that it was those changes that caused this to occur. I think there may have also been
some graphical changes around that time as well and if so this may be a result of those changes.

Also it still does it even if I do not switch tabs, usually I see it occur in the same tab that I have
been using for hours while hunting pirates.

Maybe this is not a bug any longer as it has gotten much better in the past week or so. But when I
first started seeing this I would open a new completely different browser (I have 6 web browsers)
from the one that I was using and it would still be there. As of late it quickly disappears with a page
refresh and does not appear to be showing up in a new browser when opened.
Perhaps this issue is now fixed.

Partially done again) All new cases please describe here.

Fixed.