Got any pix?
Sometimes in corners the gelcoat is sprayed too thick and simply cracks.
Otherwise, if there is flex in the area (transom) you may have issues. If it is not from your transom going bad there must be flex from something else. Aside from replacing the transom here is what you would have to do (most likely) to get rid of them:
-grind out the area down into the glass
-lay in some new long strand glass an wet it out with resin
-regrind to smooth
-fill to just below the gelcoat
-fill with gelcoat (or spray the area)
-sand with 320, then 400, then 600, then 1000
-buff
NO FUN.
You can try to fill with gelcoat puty (gelcoat, sanding aid, thickened with cabosil), but they will likely reappear.
Let me know if you have any questions.