Chakotay says that the shuttle's shields had collapsed. That's why the plasma bolt was able to kill Neelix, but the shuttle is hit by at least two more bolts that
hit the shuttle while it is retreating, and it appears that the shields deflect the bolts and the other bolts do not appear to penetrate the hull of the shuttle.
In this episode Seven displays the ability to raise the dead using nanoprobes! Or at least someone who's been dead for no more than 18 hours, 49 minutes, 13 seconds.
Given this, no-one that Seven can get to and inject with nanoprobes should stay dead for the rest of the series. Needless to say, they forget this major development.
As Neelix leaves the mess hall for the last time he takes off his apron that has his communicator badge on it yet when he arrives in the transporter room the communicator badge is back on his clothes.
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