Writing that it has an alarm doesn't seem to be catching maintenance's attention. Get a keychain, something bright and unmistakable, maybe a big red stop sign, or neon colors, you can use one color for pet homes, another for alarms.
The other option is keeping a unit profile card that goes with the maintenance tickets, lists the unit, resident, pets, etc. and highlight the important things.
With regards to crediting the tenant, it depends on what the lease has in it. If you have a clause or addendum for security systems, check there first, you may not be responsible.
Has this been reported to you before, if not, well I'm so sorry that it happened and thank you for bringing this to our attention ... it will be addressed.
If it's been reported in writing to you before... then maybe go half on it if you don't have any exclusions on the lease.