This is similar to the bug I reported about the spell Dharma's Party which Jordan did not learn. On my first couple of playthroughs when I defeated the headmistress in the Hotel of Ascension Clea learned the spell 'I can see you'. I installed the current version after I had done that, and had the problem with Dharma. I am now replaying it and so have come to the Headmistress for the first time in this version and Clea didn't learn it, nor did Shiro, even though both were in the active party. Is it random whether they learn it, or is it meant to happen?
The other thing which I keep forgetting to mention is the dialogue of the save priest in Exelion. He says that as the party has come from the south .... But in fact, they've come from the north.