Your deposit should have been protected in one of three deposit schemes, set up under a law which came in about 4 years ago. You should have had a letter telling you which scheme the deposit was in within 2 weeks of it being done. The agents should have dealt with this when you took the tenancy. Any dispute over return of the deposit which be dealt with by the scheme.
If you have never had any notification of the deposit being in a scheme then the agent is almost certainly at fault & you could conceivably take the landlord to Court - but there are dangers in doing this.
Look up Shelter on the net. They are a specialist housing charity & have an advice line which can give you more details.
Having said that, if there is a build up of limescale in the toilet leading to discolouration it almost certainly means your cleaning regime has not been adequate, so it is reasonable for you to have to pay to put it right. However, nearly £300 seems exorbitant.