I can't seem to locate a specific topic on this, but I have read about this before, specifically for KLAS. However it will also affect all airports as it is just the way that the game engine works.
Ill try and do my best to explain the situation:
When a flight calls for a pushback, the sim looks in the schedule to see if there is a flight that can replace it as the gate. Without any modifications to the schedule, some of the inbound flights would not have a gate to go to because of all the traffic idling at gates; and because there is more inbound flights than gates. When the sim recolonizes their is no gate for a flight, it will simply delete the flight from existence. In the output log file, this can bee seen with an error showing "no free terminal" with its call sign.
Since you added a bunch of extra departing flights in a short time, these "no free terminal" flights can now be assigned a gate; allowing them to come in. With the extra flights now coming in, shooting gaps at KSAN becomes nearly impossible.
As others have said on this website, the only way to fix this issue is to use snippet files from custom schedules that be be found on this website. A snippet file is simply a schedule file that has flights for only 3 hours, not an entire day worth of flights.