Yes, you are being over protective, no need to worry, she is fine. Often the first few sets of leaves can be weird in all sorts of ways (odd shapes and strange markings) and not necessarily due to anything, just that the plant is still figuring out "what this growing thing" is all about.
Sometimes marks like these are the result of people spritzing their plants with water in a misguided belief that cannabis is a rain forest plant and they need hyper humidity, which it does not. The water droplets on the leaves then act like magnifying glasses and scorch the leaves leaving brown burnt spots, so if you are spritzing, then stop. The only time spritzing leaves is acceptable is when cuttings/clones are taken and they have yet to develop roots. Spots can also develop from the same reason (water droplets) inside "humidity domes", which are again totally not required for cannabis seedlings, which need good air supply and air movement to develop properly.
Hope this helps, Organoman.