It's just the nature of the beast. 3d filling is tricky I'm finding. The primer base coat will tell on you. I would do a nice sanding and shoot it again. The cracks usually are from not getting all the debris off. I like to wipe it with mineral spirits before I shoot. Give her a good bath, let dry and wipe with the spirits. It will dry on its own and then I shoot. I also like to use a soft tooth brush while washing. Especially in corners and grooves. I did find using the xtc 3d print coating worked well for the obiwan but not so well on the kylo because of all the detail. I have to use my picks and needle files to clean it up. Your saber is a flat smooth area so this coating would take more than half the work away. Too bad you didn't live near by, I would just give you some.
As far as the seems go, I like to file them BEFORE I fill them in. Once you glue joints togetger, if you file them smooth, you will be surprised how little filler you need. Alot of what you may see are the imperfections from the joined pieces. It's nothing you caused, but simply the alignment issues. The file will level them off and once you fill and sand they start to disappear
Still it's coming along nicely so just smile and give it a couple more passes. You will have it perfect in no time.