The problem I had with Python was that there were plenty of places where, because everything is an object, I found a number of areas where things like integers were copied by reference rather than value. Maybe it's better now and maybe I wasn't doing things The One True Python Way, and it has been a few years, but I remember being really puzzled by that one.
Re^3: I want you to convince me to learn Perl
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well, one of my first languages was Pascal, where you have to tell your subroutines whether they get their parameters by value or by reference. That possybly had made me more aware of this one.
Which means, when I use sort, I have to pause thinking about whether it modifies in-place (Python) or returns a sorted copy (Perl)...
copied by reference
is just plain wrong terminology. References are used to avoid copying.
Don't even think in such terms! That impedes yourself, and then no wonder you're puzzled... regardless in which language you program.