Unfortunately, you must have not seen one of the dozens of episodes or movie scenes where ships were knocked out of warp by getting hit by a torpedo salvo. It happens all the time in the Trek world. Someone tries to run away, and you jump to warp and follow them. If they travel at a slower warp speed than you, then you run up behind them and start attacking. There IS a difference in warp speed, if you didn't know that either, lol. Warp 9.5 is faster than warp 8.0. Don't you remember the captains "pushing" their ship to maximum warp to escape something? If they could just warp away and that's it...they would never do that. They would move at the slowest warp speed, so that friendly ships can respond to help them.
Anyways...turn off your auto-grouping, it's on the teaming menus when you press "O." There's three drop down menus that select options for auto-grouping and looting. That should help.
Personally, I love it. It adds to the immersion of the game for me. Every combat situation gives me skill points, so it makes no difference whether I spend time killing some Klingons in a random battle....or I spend time killing Klingons while on a patrol.
If something was knocking you out of warp thats fine, however half the time you get sucked into these you get a message "Hey thanks for beating them back!" basicly the only time you SHOULD get sucked into these is when the event is going on, not after its finished.
Not to get all sciency here, but how the hell does a ship traveling faster (or even orders of magnitude faster) than the speed of light get hit by a projectile weapon?
We've seen how hard it is to implement an anti-ICBM missile defense shield because the ICBM is moving faster than any missile is capable of intercepting.
According to "trekkie" science, A torpedo fired at warp grabs a handoff warp field generated by the launcher and the ship and continues on with the use of it's onboard sustainer engine. Its not powerful enough to enter warp on its on though, but can reach high-sublight speeds when fired out of warp.