A quick search appears to indicate that this is a common issue on this particular model of Civic.
The bolt does not want to come out all the way because the heat from the engine over time has liberated the plastic female housing that it threads into.
To remove it you need to figure out a way to keep the plastic from spinning when the bolt is turned, as per the advice of someone who's been there, done that:
The heat from the engine has weakened the plastic around the bolts that hold
the screws in place. As a result, when you attempt to turn the screw,
the bolt isn't held stationary by the plastic as was intended.
Instead, the bolt spins, and in my case, this spinning caused the
plastic surrounding the bolt to split in places.
The solution is simple: find a new way to hold the bolt while
unscrewing the screw. My mechanic and I just broke off the plastic
around the screws enough that we could fit a wrench in to hold the
base. Of course, this won't fix the problem permanently, and will
only work if some of the screws are not suffering from this condition
(in my case, the screw in the center and the two screws on the side of
the box opposite the engine were still usable, and are now the only
screws that hold the lid down on my air filter).