It's not unusual. The clearances become smaller as the engine wears.
That's why it's so important to check them, since if they get to zero, damage to the valves and seats begins. As the engine warms up the clearance increases, so the first signs of a problem show up during cold starts. Starting gets more difficult and it doesn't run well until it's warm. You did the right thing in checking and adjusting them.
https://faq.ninja250.org/wiki/How_do..._the_valves%3F
https://faq.ninja250.org/wiki/Ninja250_Howto