I'm wondering if it is indeed nute burn.
Even 1/20th strength is not needed for small seedlings, and if you're just spraying the bottoms & sides of the cubes, the nutes will stay in the rockwool and continue causing damage.
**edit: I missed the sentence where you explained that you'd flushed the cubes, so this entire post may be of no use. Mea culpa.
One of my MTF plants has a similar light brown spot on a couple of places on one of the leaf margins, just like yours (except yours are maddeningly symmetrical where the light spots are), that appeared not long after the first diluted feeding (Jack's Classic "All Purpose" 20-20-20 @ 1/4-teaspoon per gallon which is anywhere from 1/4th to 1/8th the recommended dosage for a healthy adult plant). That tells me that I have fed them all they can handle, plus a little more, so it will be water only for it's next watering.
Not as big of a deal on a larger plant, but can be devastating for a tiny seedling, especially if the nutrients are still trapped into the rockwool.
Just a possibility?
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*Also, MTF has a habit of sometimes producing variegated leaves (streaks, patches, and even one whole side of a leaf starting out albino white), usually later on in the growth cycle, but can happen any time due to some aberrations in it's genetics.
I know it's not happening right now to your plants, but it might later on. The variegation usually corrects itself and doesn't affect growth.