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It sounds like you are using photo-sensitive board so I assume the negative mask has the holes where they should be. If that's the case, it sounds like you did not etch the copper for long enough for the fine detail (such as small holes) to fully dissolve.
There is an optimum time for etching. If the time is too short, the fine detail in the image are lost, this might include small copper areas like the holes in pads. If you spend too long etching, parts of the copper you really want to keep will start dissolving.
You still haven't told us what proces you are using. It isn't normal to electro-plate PCB tracks, usually the unwanted copper is removed rather than tracks and pads plated on to blank board.
Does your artwork clearly show the holes ?