When beaming down on Cure Ground, your science officer I believe informs you that nadion radiation (Or some other form of handwavium) is affecting cover and bubble shields, and they will be dramatically less effective, but personal shields are fine.
And thus why they had to put a stop to it. If they let it remain, players would just pwn the puzzles and move on within 10 minutes. Its supposed to be a challenge.
The handwave is in the explanation of why. The old version said there were nanites in the air itself (or radiation) that degraded the domes/shields by "eating" their power up very very quickly. Borg Domes/Shields are of course unaffected (adapted).