I edited your picture to illustrate a few visual things you might be missing;
Firstly, your plot is 17x17 squares. Although it might seem like some tiles are missing in that top square, it's a visual illusion. The plot is still 17x17, as illustrated by the numbers I've added. Secondly, the Northern and Western walls sit actually outside the plot when customized. This is normal, and just how they tweaked the perspective to make it look prettier. But when the walls are not included it makes it look like the floor above isn't aligned properly. You can see however by my tracing the edges they align correctly with the floor plan below... but when I traced the bottom line on the lower edge of the tile, instead of the top like the two above, it throws the apparent alignment off again. It's just an illusion again though.
Without seeing what you're doing, all I can say again is that, until there are walls in the corners like the bottom and first floor, the tiles will remain Orange and Illegal. If I remember rightly, it may delete the orange floors when you try and Commit the house, because they aren't valid. That's not the same as not "filling", it's trying to commit only the legal placement. They're filled in the Editor plan however. They just don't stay. What you need to do is remove all the Orange
before you commit to placement. You can save 1 back up so even if you get it wrong, don't worry. Just test and tweak until there's not a single orange square!
