Without seeing it, hard to say. If there are gaps between the top plastic cover and the bottom that allow air into it from the attic area, could just be condensation from a temp difference inside and out.
Could also be a leak around the edge of the sealant on the top cover allowing water down into the skylight.
After checking both for hairline cracks, I think I would reseal the roof top cover very well, open the inside and seal any roof access points in between with some aluminum tape like you would for AC ducting and continue to monitor to see if it persists.
2020 Chevrolet 2500 LTZ, 2019 Forest River Wolfpack 23Pack15, 2014 EZGO Golf Cart.