There are a number of known issues with Spoutcraft; some of which are tracked, and others of which are not. Detail anything you run into here.
Entities lose their skins
After logging out and logging back in, you may sometimes find that some of the custom entities we have will revert to normal Minecraft mobs in appearance. They're still the mob you originally saw; the skin is just gone.
Custom pickaxes have no durability & behave strangely
Yeah... two spout limitations in one here.
Custom foods are eaten immediately
Another spout limitation, sadly. These limitations should go away when we move to either Minecraft 1.3 or the official Spout server.
Know anything else?
I know there's more than these, but I can't think of any at the moment. If you know of anything, the wiki's open.