Those are called leaf galls. Something has been chewing on the tree, and the tree responds by making galls. This article talks about galls related to insects and mites: http://www1.extension.umn.edu/garden/insects/find/insect-and-mite-galls/ Here you can also find info on galls caused by other things (bacteria, viruses, fungi, etc.): http://waynesword.palomar.edu/pljuly99.htm

Thank you party_music. I do not think they are in want of water, I was actually afraid I was overwatering them. I've been watering them well at least once a week, sometimes more. The soil never really dries out. I planted them in "regular" potting mix (I do not recall any specifics, but I don't think it was anything fancy or special). I had the same thought about nitrogen which is why I fertilized them. At this point I think not allowing them to go dormant was my main mistake. Incase they live (or if I try this again) how do I "harden them off"? I live in Northern Nevada (at the base of the Sierra near Lake Tahoe) so it does get quite cold in the winter. That's the main reason I kept them indoors, but I now realize that may have been a mistake.

According to the "book" and what I've read thornless don't yield as much. Whether it's enough to matter to the average homeowner I don't know. Also IME Persian Limes (especially) & Key Limes are very underrated for their cold hardiness. TRUE Lemons are over rated. I have about 20 citrus trees in the ground and my Tahitian lime is one of the hardiest & most cold hardy here in zone 9B. The only citrus trees I have ever lost to low temps were a full sized Harvey Lemon and a mid sized Varney Navel tree back in our record 2010 freeze here when he got down to about 20. Nothing else even got burned. I have seen a lot of nurseries saying Tahitian limes are cold sensitive and I have not found that to be the case. Lemons I have.

Do not add soil to the top of what you have. You'll bury the root flare. You will need to do a full repot but not right now in the heat.