The purpling on the underside of the top pic is a phosphorous deficiency. Two possible causes - lack of sufficient P in the soil OR root damage that prevents P uptake. Give the size of the plants relative to the container they are in I would put my money on both problems. But could you tell us the age of these plants, their height, and the size of that container please? I suspect the container is far too small and the plant may be rootbound or will be shortly and it is starving as a result.

The damage in the last two pics could be sun burn or it could be nutrient deficiency. The problem with using granular fertilizer products rather than liquids in containers is the nutrients are not available to the plants until AFTER they are pre-digested by soil bacteria (if organic) or well dissolved in water (if water soluble synthetics. So "sprinkled Garden-tone (an organic) for vegetables on top of pot and watered a few times since" provides them with no usable nutrients. Your container, no container, has no beneficial bacteria to pre-digest dry granular organic fertilizers.

Dave

Thank you for your responses!

I have started to acclimate them for the past week or so, taking them outside and leaving them there for hours. I also sprayed once with copper fungicide as i thought brown spots are signs of blight.

These seedlings are about 4-5 weeks old and are sitting in 4 x 4" cups.

Seedlings are 9" tall.

Was about to transplant them permanently outside tonight or tomorrow but they look very tired. My initial concern was that its either bacteria or fungus

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A good example of why including your location and many more details on the plant age etc. is vital. I would never have guessed they were still seedlings only now being hardened off from the initial post and photos.

In that case the purpling is common in seedlings as their roots haven't developed enough yet to handle nutrient uptake all that well and the damaged leaf in your latest photo could easily be from sun or wind burn. Just remove it and get that seedling planted asap and fed well when planted. All that leggy bare stem will benefit from being deeply planted as well. Bury it right up to just an inch or so below the top set of leaves so roots can develop all along that bare stem.

I assume they are going into the ground, not a pot? Be sure to strip off all that fiber pot before planting them.

Dave

On my way planting them!!!

Super exited that I don't have to throw these away.

Some of my seedlings got a bit too big in their 4x4 containers before I could plant them out and looked similar. They are now in the ground and looking so much happier. Gave away a bunch of extra plants, and everyone has commented on how they have perked up quickly with repotting/planting into the garden. I'm sure they will be much happier once they are in their new homes!

I think so, here they are, what should be much happier than they were seedlings.