Can be a number of things yellowing your seedlings. Stuff like, ph swings, under/overnute, bad lights, overspraying...

The nutes in your MG soil will last a while. You shouldn't need to add nutes till about a month after your next transplant, which should be in something like a one gallon pot. Going from peat pucks to peat cups, you might be having a low ph problem. (peat lowers ph)

When you do transplant from those peat cups, peel away as much of the cup as you can, but don't risk root damage. Yes, the peat cup will eventually break-down. But until that time, the roots will be restricted. And if you let the peat cup dry-out, it can become tougher for the roots to penetrate.