We know that a forcefield can be designed to hold just about any arbitrary shape - that's how holodeck illusions are created. But that may take a lot of extensive machinery dedicated for the complex purpose. A cell wall type forcefield may well feature such dedicated machinery, too, for the purpose of "selectively accessing" the interior. But the fact that Soran's forcefield in ST:GEN was truncated at a rock arch was most probably a malfunction, a failure of planning, a shortcoming of a simple field generator that's only designed to create a plain old dome...
The gaps in the defensive shielding of starships would definitely be design faults - but in "Preemptive Strike", they weren't real. Our heroes just fooled the Maquis into thinking that Starfleet had forgotten to patch this potential hole, and in fact deliberately opened up the hole to make it more attractive. And in "The Wounded", the shields of the Nebula class ship didn't have holes in them as such: they merely had a characteristic that allowed a careful intruder who knew his way around Starfleet ships in general, Nebula class ships in particular, and this very specimen of the class especially, to squeeze a transporter beam through - in an excruciating, multi-minute procedure that had no combat applications.
Timo Saloniemi