hey im working on a tutorial and ive stumbled upon another problem that i cant seem to quite fix.

im creating an aeroplane, ive made polygon cylinders for the windows and ive combined them all.
i used the boolean difference tool to subtract the difference from the plane and the tubes to create my windows. However the problem is the difference didnt seem to work completely...??? out of lets say 40 of the windows only 20 actually appeared

https://img16.imageshack.us/i/22352224.png/

ive uploaded the image to give you guys an idea of what happened.