Those intercept missions you ignored were probably flights inbound to your airbase, and they likely bombed your airfield. As said above, roll back your take-off times closer to the campaign clock and it should work. I would do Taxi, rather than Take-off if not ramp starting, just to have a little time to make last minute checks. I prefer ramp starts. :razz:
Edit: If you are in fact, having the “bombed airbase” issue (I’m assuming this is a fresh KTO campaign and you are letting the AI frag missions), you may want to concentrate on air superiority for the fist day or so. Protecting your air base and striking the FLOT are Day 1 missions for a successful campaign start. Let the AI handle the suicide missions or turn off Set by HQ in your squadron page and frag your own missions and save your airframes by not letting AI fly them. HTH