It looks to me as though the marks you are seeing are resulting from your resin shrinking from the inside out (hottest part first) as it cures, while the resin on the outside (the coolest part) is still somewhat liquid, thus pulling away from the mold and leaving marks due to places where it has still adhered to the mold versus where it has pulled away. So one option you might look at is to try to find a type of resin that shrinks less (which typically means it also takes longer to cure), or try to cure your resin more slowly at a lower temperature. Another approach is to try to heat the outside of your mold (blowtorch? oven? hot air gun?) so that the resin cures first there, thus pulling away from the mold more uniformly. Another (generally always advisable regardless of what else you do) is to use spray mold release into the mold before you use it so that the resin won't try to stick to the mold and will just pull away everywhere as it shrinks, instead of pulling away unevenly as it has apparently been doing.
I would be cautious about using a different kind of resin (e.g. 5-minute epoxy) to fill such gaps: the other kind of resin may cure a different color, or may eventually turn a different color due to UV exposure (browning) at a different rate than the resin you used for the sphere. This may be noticeable, either initially or over time. The other resin having a different refractive index may also be an issue, resulting in distorted light transmission instead of a nice clear "spherical lens" effect.
If I found myself with your problem, I would probably try to use the resin I already had to solve it, either by applying it with a paintbrush to fill the gaps and then sanding the sphere smooth again, or by putting some mold release in the mold, then pooling a little bit of resin in the bottom of the mold, and then painting the surface of the mold with resin, and then painting some resin on the sphere (filling the crevices), and then re-inserting the sphere into the mold (being careful to watch out for bubbles!) so that the little bit of resin in the bottom of the mold is displaced by the sphere and is forced to flow up around the sphere (hopefully taking bubbles with it) until some pours out the top of the mold. (Essentially, re-mold the sphere with some additional resin, so that gaps will be filled.) Hopefully the second time around, the amount of shrinkage would be minimal since such a thin layer of resin is being cured.
Another approach would be to just put the sphere into the mold and then pour resin over the top of the sphere, allowing it to flow down around the edges of the sphere into the mold until it fills the space between the sphere and the mold and covers the sphere completely. This will only work well if your resin is relatively thin, however.