This is why the Super Bowl is played at a neutral city (unless it accidentally isn't). Half the tickets for one team, half the tickets for the other team, and half the tickets for the rest of the world that wants to go to the game as well.
Also, it's standard procedure to move everybody around for playoffs. Let's say you have 20,000 full season ticket plans, then 10,000 Sunday plans, 10,000 Saturday plans, 10,000, weekday plans, 10,000 weekend plans, etc. That's already 60,000 seats, and Citi Field only holds 45,000. That's why everyone gets moved out of their seats, because it's the fairest way to get everyone a shot at at least one game even if they only had a partial plan.
It'd be the same with NYCFC if we have a home playoff game next year, and it'd be even "worse" if we make it to the final. I'd just be happy enough to get inside the stadium, wouldn't be too concerned about getting my same seat.