Answer: yes, you can repair both buildings and vehicles with the repair tool - I've done it before with both pod beacons and shield generators., as well as the heavy turret.
Not sure why it wouldn't let you? Unless they've changed the code so you have to repair at the control panel... try that. (Every building has a control panel so you can upgrade/reclaim it)
I've had a total freeze a couple of times.
It *is* still a Beta, so you need to report any bugs, glitches or freezes here:
http://community.eu.playstation.com/...td-p/14142505:
(PS, being run over by Cadder isn't a bug
)