Ok so yesterday I practiced saxophone for about an hour and a half. Afterward, I started practicing flute. Here were the problems:

1. Airy tone
2. Pitchy
3. Octave jumping/overtones that i didnt mean to play
4. Bad embouchure

I know its because I just got done playing sax, but...why? Can it be improved, does it take practice to switch between instruments? Just wondering...

Just like everything else, changing instruments takes practice...just concentrate and focus, blow a few long tones on flute when you first pick it up and find the 'sweet spot'...hold it for a full breath several times, concentrating on minimizing your air flow.

see if you can locate a good doubler in your area, someone who plays flute/cal/sax professionally, they can advise you as to how better adjust, I have worked with some amazing doublers, and they do things differently than we do...

Until you are aware of the embouchure issues, you should take a break of around 10 minutes when switching instruments. In addition, if you are new to saxophone, then you'll find your lip (and possibly jaw) muscles are just tired after playing and need time to recover (more than 10 minutes). It is probably a good idea to play both instruments more or less daily at least while your embouchures are still developing.

Well, im not new to sax(playing about 3 years now) and flute I recently picked up(last year). I did play my sax then picked up flute and my jaw felt weak and uncomfortable after playing for around 10 minutes, which I guess is why none of the high notes were speaking and I had bad control. I guess I should limit myself to one instrument a day?

sorry meant to say high notes WERE'NT speaking.

don't limit yourself to one a day it just takes practice try haveing a short break inbetween the switch (have a drink and a few minute breather) then pick up the other instument and make sure you warm it up.
That is just a suggestion as i am not a switcher myself but i know some one who does and she said whe she first started she needed a quick breather before she picked up her flute.
But don't gt fustrated it just takes a bit a of practice.