Is it a small fragment of the red targeting bracket in the upper left of the screen? If so, I've had that too. I know a few other pilots who've had it as well, so it's likely a bug. As for the audio hiccups, it could be drivers, it could be a bit of spyware or a virus causing issues (only likely if it does this in other games/programs too), it could be the brand of card itself. I used to have an ASUS Xonar, POS caused no end of bluescreens under Win 7. Problem was, trying to update the drivers made it bluescreen as well
So, yes. I wouldn't panic just yet
If you're using a sound card rather than onboard sound, try enabling onboard sound and see if that clears up the pauses (only do this if you know what you're doing!). I do occasionally get crackles in MWO's sound effects, but they seem part and parcel of the experience on my rig, and they only happen in MWO, so go figure. Hope that helps, and best of luck!