So I am growing a jacaranda mimosifolia. It’s been almost three months and it was getting awefully tall so I took it out of its tiny seed starting biodegradable pot and put it in a little bit bigger pot so it had more room to grow. After I reported it I noticed some of the leaves were drooping which I just brushed off as I took it to be a common thing with doing that with young plants. Well I started to noticed that the bottom leaves weren’t getting any better and actually dying, and now there are brown spots forming on a bunch of the leaves. Any help would be greatly appreciated since this was my first tree that sprouted. I can post pictures after I get off work. I just found this today and figured I would see what you guys thought. Also I have moved it out of my mine greenhouse just in case.
Also I am very new to this whole thing, but I do have 8 Delonix regia that have sprouted and are doing fine and 2 Rocky Mountain Bristlecone Pine that are very small but seem to be fine from what I can tell

Pictures?

Here is what she looks like. Only ones that don’t have it are the new leaves sprouting up top

I have some Jacaranda seedlings myself, and they are very sensitive to foliar feeding, don't do it, they die on you.
Other than that, sunburn or fungus are the other possibilities; for fungus, 3% peroxide diluted in water (1 teaspoon/1 litre) can help.

Should I do that in place of regular watering or with it?

Higgins wrote: Should I do that in place of regular watering or with it?

You can substitute one of your regular waterings with the peroxide "bath".
I do it once every 15 or 20 days.
Make sure you spray the foliage to minimize the fungal issue (IF it is fungus after all).
Good point is the diluted peroxide will not harm your plant.