Summery:
You must talk to the colonist at the top of the hill before going down the hill and beaming up colonist or else mission breaks.

Details:
The problem starts when you beam in to Hatep IV.
I ran down the hill and started fighting the borg but after fight for a long time I could not find a way in to the force field where it shows the colonist on my map. I then used the Scan Area function and it would point me to where there was nothing! but once I got to where it was pointing a box came up saying "Tag for Beam Out". I beamed out three of these invisible somethings then decided to go back up the hill and see if maybe there was anything up there to turn off the force field.

Thats found a colonist there and talked to this person. the person said to beam up 5 colonist. then it hit me, the invisible somethings I beamed up must have been colonist! the problem was it said I had beamed up "0/5" when I KNEW I beamed up three. I then went back down the hill and saw the colonist where now visible BUT there is no longer a option to beam them up!

I had to abort mission and I submitted a bug, but I imagine it wont be fixed for weeks so I would post a warning to all the other players.