I am not sure if it is a bug or something else, but this is what happens:

Normal users cannot break/place blocks in another user's protection, however if they find the ore (the protection block) and mine it the protection disables.

This happens in all version of PreciousStones and all the versions I ran them with the corresponding craftbukkit version.

Here is a copy of my config:
http://pastebin.com/qE8Tc5vy

Your config looks good. Thought maybe you had the breakable flag on your fields that was allowing other players to break the field block (they shouldn't be able to). The only explanation is that you are somehow giving all your users bypass permissions or admin permissions and so they can break anyone stuff.

I am using PermissionsEx, and this are their permissions:

 preciousstones.whitelist.*
 preciousstones.benefit.create.forcefield
 preciousstones.benefit.create.unbreakable
 preciousstones.benefit.create.protection
 preciousstones.benefit.who
 preciousstones.benefit.onoff
 preciousstones.benefit.counts
 preciousstones.benefit.locations
 preciousstones.benefit.density
 preciousstones.benefit.setname
 preciousstones.benefit.disable
 preciousstones.benefit.visualize

Maybe I can try negating the general admin permission:
-preciousstones.admin.*

Maybe they are breaking through the block with a fast mining tool that doesn't respect the block break event like wordedit superpickaxe?

No, they don't have permission for it.

No don't do that, same ids cant be "force-field-blocks" and "unbreakables" at the same time, you will cause a ton of conflicts there. Fields themselves by the virtue of being fields should not be breakable.

Actually I know what is happening. You probly have another plugin interfering. Try removing all other plugins except critical ones like (chat, permissions, etc) and trying it again. I'm pretty sure you have some sort of drop plugin or something like that interfering with the breaking of the blocks.

I now added the protection ores to unbreakable-blocks and there was a change: the block still can be destroyed and it disappears actually but the protecion does not disable now

If you're using the latest beta this is probably the reason. I used the latest CB beta build the other day and noticed tons of issues within the build.
Can you post all the group that can break the pstone blocks permissions please

Here are the ps permissions in my pex permissions file, however the problem is with users on gruop Default. The problem is not because of permission nor CB version, I think it has to do as phaed420 said, other plugin conflicting.

groups:
Default:
default: true
permissions:
- -preciousstones.bypass.*
- preciousstones.whitelist.*
- preciousstones.benefit.create.forcefield
- preciousstones.benefit.create.unbreakable
- preciousstones.denefit.create.protection
- preciousstones.benefit.who
- preciousstones.benefit.onoff
- preciousstones.benefit.counts
- preciousstones.benefit.locations
- preciousstones.benefit.density
- preciousstones.benefit.setname
- preciousstones.benefit.disable
- preciousstones.benefit.visualize
options:
build: true
rank: '900'
prefix: '&f'
SubModerator:
permissions:
- preciousstones.benefit.*
- preciousstones.bypass.teleport
- preciousstones.bypass.*
inheritance:
- Default
prefix: '&3'
options:
build: true
rank: '700'
Moderator:
permissions:
- preciousstones.bypass.*
- preciousstones.alert.*
prefix: '&5[Moderador]&3'
options:
build: true
rank: '200'
Admin:
permissions:
- preciousstones.admin.*
prefix: '&2[Admin]&3'
options:
build: true
rank: '100'