For the "dark shape on a shirt caused by wine" example, your best bet by far would be stain. I'm having a hard time coming up with any other word that would be understandable in that context.
Stain strongly implies that the color was changed by a strongly-colored agent, usually a dye or something similar. For example, we would also use "stain" to describe treating wood to give it a darker color. "Stain" comes from the old french "desteindre", meaning "to tinge with a color different than the natural one". This would fit your "wine on the shirt" example perfectly, and similar marks caused by dye, ink, food, etc.
If we're looking at a differently-colored area of a paint job or finish, there are several words that could work:
A crack or breach, a gap or fissure; a defect of continuity or cohesion.
This would in general be good for your needs, but especially appropriate if there is a defect of continuity, i.e. most of the finish is uniform, but part of it does not share continuity with the surrounding area.
An uneven patch of color or discoloration ... An irregularly shaped area.
This would work well for your definition, but anecdotally I feel it's not used as often as a noun - I usually see this as the adjective "blotchy".
A small flaw which spoils the appearance of something, a stain, a spot.
Blemish fits your definition, but is often used in the context of skin (e.g. "...to minimize the appearance of facial blemishes or pimples, use a concealer with a dry texture...").
There are additional words that could be used when describing errors in applying a finish or paint job (see chip (#2), scratch, smudge, crack, etc) depending on the specific type of flaw.