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Last summer, I repaired several screw holes in my transom. I removed the screws, drilled out the holes and inserted a wooden dowel insert to fill the hole and then used Spectrum Gelcoat Repair Kit to finish the job. Before adding the dowels, I notice there was a very slow drip of water exiting frm the holes, a drop every few minutes. I let the holes drain for several days before adding the inserts and gelcoating. I thought I had done a good job but now I have noticed that there is a black, acidic residue that appears at the repaired holes, and also the repairs are showing hairline cracks that form around the perimeter of the repair. I will need to redo, does anyone have any advice on what went wrong and how to proceed on the redo? I appreciate any help!

Thanks!

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Sounds to me like you need to open it up and repair the wet area(s) of plywood. Could be an easy job with a grinder, some filler and re gelcoat. But it could be opening Pandora's box. Rarely have I come across a wet screw hole that was limited to a small area. If it's not delaminating or showing big stress cracks and the boat otherwise has no signs of being waterlogged, it's probably not a huge concern.

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You did not mention if you coated the wood dowels with an epoxy or polyester resin which would secure the dowels and seal the repair. Maybe you just missed this step or you forgot to mention it? If water was present I would have used epoxy to seal the dowels/repair. After sealing the repair then you would repair the gelcoat.
Gelcoat does not stick to epoxy very well so you might need to sand/grind down the epoxy so that area is lower than the surrounding area and then apply polyester resin and then your gelcoat. Others might have a better idea but that is how I would repair it.

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Wood acts like a wick and will distribute moisture given time.

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I would always avoid a repair over a wet substrate. There will always be ramifications as in your case. It's like putting a band aid on it.