Have you switched to your level 2 limits? Once you learn the first limit for the next level, you must switch to that level to be able to use it to learn the next one.
Looks like it may be the problem to me. The same thing happened to me during my 1st playthrough 7 years ago, until I figured out I had to switch levels. I think there is a limit menu for it (can't recall, been too long since I played), and once you select the next limit level, you can't use the limits from the previous levels (with the exception of Tifa).
If you did this and it's still not working, then I have no clue what can fix it.
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