Actually, the phaser thing made perfect sense to me.
On the Enterprise, Reed and his security team shot one of the bad guys with a phase gun and it didn't kill it. The borg adapted and transmitted the info to the other borg who was just around the corner. Thus, both Borg were adapted.
On the Borg ship, the first few Borg Archer and Reed encountered were alone and were taken down by the first shot. Presumably, they had time to neither adapt or transmit any information. When they encountered multiple borg at once, they shot the first one or two, but the others were present to analyze the beam and adapt, which they did and their weapons were no longer able to penetrate the Borg shields.
Seems logical to me.