The full description of the Fabricate spell:

You convert raw materials into products of the same material. For example, you can fabricate a wooden bridge from a clump of trees, a rope from a patch of hemp, and clothes from flax or wool.

Choose raw materials that you can see within range. You can fabricate a Large or smaller object (contained within a 10-foot cube, or eight connected 5-foot cubes), given a sufficient quantity of raw material. If you are working with metal, stone, or another mineral substance, however, the fabricated object can be no larger than Medium (contained within a single 5-foot cube). The quality of objects made by the spell is commensurate with the quality of the raw materials.

Creatures or magic items can't be created or transmuted by this spell. You also can't use it to create items that ordinarily require a high degree of craftsmanship, such as jewelry, weapons, glass, or armor, unless you have proficiency with the type of artisan's tools used to craft such objects.

These are all the limitations of the spell.

Walls are objects (like most parts of the environment that aren't creatures), so a part of a wall or a piece of flooring (e.g. a wooden plank) would be considered an object as well. Depending on the size of the chunk of wall, the material it's made out of, and the level of craftsmanship making such a wall piece would require, Fabricate might be able to make it.

In your particular example, it's a stone wall, and thus you would only be able to make a Medium-size piece of wall (that fits within a single 5-foot cube) with one casting of the spell. Your DM would also need to rule that it doesn't require a high degree of craftsmanship to make. And of course you'll need the stone in some form (whether in rubble or from a boulder or something), since that's the raw material that is being magically converted into the new form.

Also, keep in mind that nothing about the Fabricate spell attaches the object you create to anything else. Even if you meet the above conditions, you'd need some way to place the chunk of new wall you've made into the hole in the wall, and to secure it there.

Like many rules issues in 5e, there's no actual answer to this in the rules: we're not told whether trees count as creatures, and we're not told whether they can survive being rearranged by a fabricate spell. You're welcome to rule that this is possible if you want -- it doesn't seem to open up any avenues for abuse, and having living bridges or living houses seems like a fun bit of roleplaying.

But there's a deeper issue here: it sounds like you're asking about the capabilities of your NPCs.

Your NPCs are not actually bound by the rules in the Player's Handbook. You can give them whatever abilities you want. You could decide that an NPC has a custom spell, or that they have an unusual class feature, or that they took a custom feat.

One example of this in action is the 5e monster "Knight", which is CR3. It has 8d8+16 hit points, has the multiattack feature, has a proficiency bonus +2, and has a special ability called "Leadership". This is not something you could build using the PHB rules.

You can give your NPCs whatever capabilities you think would be fun and interesting. (You might prefer to use custom spells for this, though, rather than adding additional functionality to spells the player characters might have access to.)