Hmmm , odd.

I can't say what's appropriate or what's supposed to happen. All I can do is compare notes.
Notice : I am playing blue side ,also a different map and campaign.

But , before the recon & insertion mission , I did wipe out everything at the base.(buildings ,radar dishes ,fuel tanks ,etc.)
Also destroyed enemy helicopters sitting on the pads in the nearby Farp along with fuel, ammo ,& anything else that was shootable.

Maybe one or more enemy helicopters were on a mission when you destroyed their Farp. (Making it an incomplete capture until that helicopter or helicopters are destroyed)

I have noticed that after my insertion , the troops ran around for a few minutes then the destroyed enemy Farp turned from Red(enemy) to Blue(friendly) ,but the enemy base still remains Red and on the map.

Another recon mission appeared for that particular base to see if rebuilding was happening. But no more insertions.