The main "window" height is calculated based on the browser window height, which creates 2 scrollbars, one for the website and one for the "squad-build-tool" div, which is a pain when you have more than 2 ships becuase you have to switch the scroll from an area to another to see either the total points or all the squad. I removed the height manually so I don't see it anymore, but I think it should be the way-to-go solution.

Yes. It's perfectly fine to scroll the browser window. We are used to internet pages being like this since the 90's.
We don't need you to constrict all the content into a div, then scroll the div.
It would also allow people to scale down the size of everything with CTRL+Mouse Wheel Down and make everything fit on the screen at a time, removing one of the gripes that many people have about the user interface being oversized for a computer screen or tablet.

To the left it shows how a 5 ship squad currently looks like when the page is zoomed out. You can not see the last two ships because they are inside a div with scrollbar that hides them.
To the right is the same only with the attribute that @Nevetz told you to disable removed. Now the squad takes the whole screen, as it should.