Happens to me every time I water, I'm in coco using smart pots. I just move some soil over them to keep the light off of them and move on. As long as you can keep the light off of them should be ok.
Just a random guess, I'm a noob. But could it be because your soil is having a hard time draining, so most of the water it staying on the top? Causing the roots to push upwards?