Motub has hit it right on Jinta.
Turn off the AI. Most characters, particularly fighters, have some degree of built in AI anyway. You should also go to the scripts page (I don't remember exactly how to get there right now but it is from the same screen that shows each character's information). Set the scripts to "none". The AI (which is the lit up face in the bottom right of the screen) will be on each time you load a game so you must get in to the habit of turning it off each time you load.
Other than that, pay careful attention to the spell descriptions. If a spell mentions enemies or enemy creatures, it will only harm them. If a description only says creatures or doesn't specifically state enemies, it will harm anyone. Some spells only affect creatures with a low level of hit dice, so if your characters are of high level, they may avoid the effects just because of that. Generally, monks and rogues are best at avoiding area spells.
My personal style of gameplay is to use area spells like fireball right at the beginning of a battle, when the enemy is usually grouped together. For where I am right now (in the Goblin Warrens) this works great on gobs and orcs and will usually take some out right away, while damaging the stronger ones pretty well. As my characters advance in level, I will be more likely to send area spells into the midst of certain characters, like my monk and rogue.
If you haven't already done so, go to the options page and check out the auto-pause settings as well. They may prove helpful in some situations.
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