It's always a little tempting to simply setup your strongest units as human shields and let your enemies crash into their own doom while in Dungeons, but this, unfortunately, will cause great fatigue to your soldiers. The more you have a single unit fight in battle and finish off your foes, the more stamina will be drained from them. If you aren't keeping track of this statistic with your soldiers - the happy face near the top left corner of their character pages - you'll quickly find them taking a penalty to their overall Health until they have eaten some food.
But keep in mind that this only matters when you're battling in Dungeons. In most battles, fatigue will literally have no effect at all to your units. So, while in dungeons, you should always try to let your weaker units fight and finish off enemies. This will allow your better units to stay energized, as well as help you weaker units get stronger. Having an army full of very good units is always better than one that only contains a few great ones.