I lived in a number of apartments in several states, with and without animals. As far as I can tell, most apartments have no pet policy and those that do, usually charge an extra cleaning fee. Many pet owners do not mind paying that extra fee, because finding an apartment that allows pets is not easy.
Enforcing the pet policy is another matter. Many landlords enforce it selectively - i.e. when the tenant pisses them off for other reasons, but look the other way when the tenant has been "good" (i.e. paying the rent on time and not bitching). So if that is your case and you can prove it, you may use selective enforcement as a defence although I am not sure how effective (Justin?).
Another simple strategy is to flatly deny, if plausible, that you had an animal in the apartment and refuse to pay the cleaning fee. That shifts the burden of proof on the landlord. This strategy will work best if the landlord asks you to pay an extra cleaning fee (rather than deducting it from your cleaning deposit) - because your refusal would make it necessary for him to go to court and argue his case, which would probably cost him more than $250. If the extra cleaning fee has been already deducted from your deposit, you can still go to small claims court and deny that you had an animal. If your landlord cannot prove otherwise you have a chance of winning the entire amount back. Small claims courts often give 50-50 verdicts in hard-to- prove landlord-tenant disputes (i.e. award about half of the amount sought by either party) so you may win about $125 back - if you have time and energy to spare.
You can also check Nolo press publication (http://www.nolo.com/) on landlord-tenant issues - found them helpful.
Wojtek