Can Eating too Little Make the Scale Go Up?

Yes if you compensatorily reduce your conscious and unconscious energy expenditure activity by more than the food restriction. Plus all the usual water weight fluctuation reasons. And more along the lines of not go down as opposed to go up.

Yes, increased stress can increase cortisol which can lead to water retention.

This isn't right on point for you, but might be useful:

http://www.bodyrecomposition.com/research-review/dietary-restraint-and-cortisol-levels-research-review.html/

...a group of women who scored higher on dietary restraint scores showed elevated baseline cortisol levels. By itself this might not be problematic, but as often as not, these types of dieters are drawn to extreme approaches to dieting.

They throw in a lot of intense exercise, try to cut calories very hard (and this often backfires if disinhibition is high; when these folks break they break) and cortisol levels go through the roof. That often causes cortisol mediated water retention (there are other mechanisms for this, mind you, leptin actually inhibits cortisol release and as it drops on a diet, cortisol levels go up further). Weight and fat loss appear to have stopped or at least slowed significantly. This is compounded even further in female dieters due to the vagaries of their menstrual cycle where water balance is changing enormously week to week anyhow.

And invariably, this type of psychology responds to the stall by going even harder. They attempt to cut calories harder, they start doing more activity. The cycle continues and gets worse. Harder dieting means more cortisol means more water retention means more dieting. Which backfires (other problems come in the long-term with this approach but you’ll have to wait for the book to read about that).

When what they should do is take a day or two off (even one day off from training, at least in men, lets cortisol drop significantly). Raise calories, especially from carbohydrates. This helps cortisol to drop. More than that they need to find a way to freaking chill out. Meditation, yoga, get a massage... Get in the bath, candles, a little Enya, a glass of wine, have some you-time but please just chill.