This maybe a noob question. But it seems lately anytime I go to use my healing BO skills in space combat it targets the nearest friendly instead of me. Even if I just have an enemy targeted, right at the moment I need to repair my hull or shields a friendly gets targeted and I have to wait for the cool down (if I can last that long) to reuse it on me, and even then I untarget everything so I am sure it will be used on me. Then I have to re-target the enemy. Is there a setting I have on that is doing this? I am currently a Sci officer flying a research sci ship.

There's a setting in your Options for assisting your enemy's target. Can't exactly remember what it's called, but it basically means that if your enemy is targetting someone else when you use the skill, it automatically casts your skill on the team-mate that your enemy is attacking.

So if you're attacking Enemy1, and Enemy1 is attacking Team-Mate1 when you use Engineering Team, then Engineering Team will cast on Team-Mate1.

Just go into your Options and change it.

When you disable that option, will the abilities just automatically target yourself?

Yes, they will.