If a lesion on the skin was suspected to be a wart but isn't, it could be a clogged sweatgland which develops excessive callus tissue with a core in the central portion. We sometimes refer to these as porokeratoses.
In some instance, a foreign body can also look or seem similar to a wart. When a small piece of hair or glass gets into the skin, the skin sometimes walls the area off and calluses over. This can look and feel similar to a wart as well.