I'm not sure how you're tending your warhorse, so in order to not make any assumptions, I'm just going to list some general things. Take them as you may.
Keep in mind that if your character's warhorse is in a state of confusion (as it seems it may be), that what I am about to say will not really apply until the server has reset.
1) Paladin warhorses are nothing like the horses you can buy for general use. They are treated as henchmen/associates in terms of how one controls them. As such, there is currently a known issue involving a character who tries to manage an ox and a Paladin Warhorse at the same time. This should be fixed in the next update.
2) A warhorse, by all rights, should be summoned when needed and released when not. So for example, if you're going into Port Hempstead for some crafting, the "right" thing to do would be to release your warhorse to the wild rather than leaving him parked somewhere. In actuality, as a henchman, that horse is going to try and follow you across area boundaries due to the usual henchman AI/logic. This can be confusing and non-intended.
3) There is also a known issue which arises when a paladin logs out or crashes with his/her warhorse still summoned, which can cause a disconnect between the paladin and the warhorse in a way where the paladin cannot call a warhorse and their previous warhorse may not be accessible. Again, the ideal thing to do here is to release the warhorse back into the wild before logging out. This too should be fixed in the next release.
If you feel any of these possibly describe the circumstances you are experiencing, then great. All you can do is be patient and try again when the server resets, keeping the above 3 things in mind. If not, and if they persist after the next server reset, please let us know as much as possible about the circumstances and sequence of events that lead up to the error condition.
As stated above, the primary causes of failure should be fixed or at least improved in the next update.