I'll try to be gentle, but my red pen is out. ;-)

The start up and spooky ending tie in well together, but the story is unfocused. The tone of the story doesn't stay consistant:

The damn dog just wouldn't shut up. It, and others like it, had recently been drafted into the space service as they had proved almost pre-cognizant in alerting crews to internal danger before anything was noted as amiss on the control panel.

The first sentence is a casual attention-getter. (And an effective one.) It's how someone might talk to a friend. The next sentence is very stilted. It's a line from a manual. The two together are jarring. They'd work great together for dialog between two characters to quickly set up their personalities, but put together as description, the sentences collide.

You also drift points-of-view. In one paragraph you go from first person to limited third person omniscient:

Fearing the worst, I had shields raised and the ship put on red alert. It might have been too late for the maintenance crew, but it wasn't too late for everyone else, the captain hoped, but at least the dog had shut up.

After that you jump around to different people's thoughts, which makes it difficult to keep track of what is going on. I also had problems figuring out which captain was which. Why tell us what was going on with both bridges? Why not keep everything focused on one ship? If they have viewscreens, we can easily get the necessary information from what the one ship sees, plus you can filter it through their perceptions and give us more flavor.

There are good touches within the story - this isn't a hint to junk it. ;-) You simply need to decide what POV to use and to stick to it; the problems will fix themselves. Hope this isn't too harsh. I'm far harder on my own stuff. Cheers!