Overwatering and fungus gnats could be at least part of the problem, and certainly aren’t doing the seedlings any good. On top of that, in my experience, roses and oil don’t mix, at least not when it comes to being sprayed outside of dormancy. In fact, the symptoms of oil-caused phytotoxicity are rather similar to the ones you’ve described. I’m not sure what a Neem oil soil drench would do to rose roots or to the medium itself, but it seems a bit risky to me.
Letting your seedlings’ growing medium get at least slightly dry on top before watering again will help if you suspect that you may be overwatering. If you do have fungus gnats, and BT-based mosquito control granules are labeled for them where you live, try adding those to your watering solution according to the directions instead of Neem oil. If you have insect or mite problems on aerial plant parts, roses are much more tolerant of insecticidal soap.