My best guess - which is just a guess - is that the seed starting mix is most or all peat and it's clumping around the roots. I can see the surface puckering as it dries. Often this is addressed by increasing the percentage of perlite in the mix as the container size gets larger; starting with little or none in a very small container and getting up to significant percentages in larger containers. I wouldn't attempt to solve this with perlite though. If I were experiencing this I'd simply repot the plants using a container soil with lesser absorption and better drainage. That will allow you to water thoroughly when you water - and perhaps even watering more often - without leaving the roots in an ongoing saturated condition, which I suspect is the problem here.
Are the containers still heavy at all when then look dry on top or are they very light?