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So you've probably got a case of (3) now. You usually don't have to make mortal something that you aren't putting directly onto the Perl stack, but sometimes it is convient to do so.
For example, you could use newRV_noinc() since you are making a reference to an AV that you just created (and thus that already has a reference count of 1). Then you wouldn't need to make the AV mortal. Or, you could decide that you like the slightly less efficient method of immediately making it mortal such that it will get freed even if something goes wrong with (or before) your call to newRV().
I'd try to avoid calling SvREFCNT_inc() / SvREFCNT_dec(), there's usually a clearer way (that is less likely to be done incorrectly). You should call croak() not printf() and exit().
Why not use call_pv() instead of call_sv() and making yet another thing that you have to make mortal?
So your original problem was two mistakes. First, av_push() doesn't increment the refcount so creating a new SV and av_push()ing it onto one array is fine (refcount starts out as and stays 1). But av_push()ing it onto two arrays would be bad (refcount still 1 when needs to be 2). Mortalizing the SV means the refcount drops to 0 later so it tries to get free()d twice.
Second, you use newRV() [which is newRV_inc()] so the AV's ref count was too high. So you had one ref-count too high and a different ref count too low. So your two choices were leaking an AV such that the AV didn't try to free up the SV a second time or properly destroy the AV such that it noticed that the SV had too low of a ref count.