This is obviously a bug which I hope will be easy to fix.
I would have to disagree: This is obviously a feature, which I hope will not be changed at all. Something as huge and compartmentalized as a Starbase ought to come online during the building process rather than being inert until the very end, and while it is unrealistic for it to have its full firepower available at the very start of the building process, it is a much better approximation of having its systems go online as they are completed than having it as a dumb hunk of metal doing nothing until construction of everything up to and including the kitchen sinks fully completes.
That said, I have to agree with the rest of you on the issue of small installations like Hangars and Repair Platform. As they are very small installations created by the crew of construction frigates rather than the crew of many (tens of) thousands living on and working on a Starbase, they shouldn't go online until completely finished.