I know this is a stupid question but...

whenever I look up calories for cooked vegetables on fitday they are considerably more than the raw veggies. Now I know cooked vegetables usually take up less room so a cooked cup of vegetables has more vegetables than a fresh cup, is that why there is a difference?

Yep.

A cup of raw carrots, cooked down, takes up less than a cup of space. So to get a whole cup of cooked, you need more carrots = more calories.

Personally, I prefer to track calories using weight compared to cup measurements, because the size you chop things up can also have a big effect on many calories you actually end up serving yourself in addition to cooked vs raw~