Hi,
all SemiAdmins receive all alerts in gray, but they haven't the permission "preciousstones.alert.*", they has got these permissions: http://i.imgur.com/ZMwwd.png
How can I disable alerts for them?
Regards.

Which specific alerts are they receiving?

These: http://i.imgur.com/tBypR.png

I use bPermissions, so I would try something like:

^preciousstones.alert.*
or
^preciousstones.alert.warn.destroy
(The ^ symbol means "Not")

With other permission mods you might use something like this:

preciousstones.alert.*: false

preciousstones.alert.warn.destroy: false

Code is very specific:

if (plugin.getPermissionsManager().has(pl, "preciousstones.alert.notify.bypass-destroy") && canBypassAlert(pl))
{
ChatBlock.sendMessage(pl, ChatColor.DARK_GRAY + "[ps] " + ChatColor.GRAY + player.getName() + " bypass-destroyed a block " + (new Vec(block)).toString() + " in " + Helper.posessive(field.getOwner()) + " " + fs.getTitle() + " field");
}

Without that permission, they cannot receive that message. They must be getting that permission somehow in your setup.