I know Perl best, so I'll pick on it.
Perl tried many ideas. Some were good. Some were bad. Some were original and not widely copied for good reason.
One is the idea of context - every function call takes place in list or scalar context, and can do entirely different things in each context. As I pointed out at http://use.perl.org/~btilly/journal/36756 this complicates every API, and frequently leads to subtle design issues in Perl code.
The next is the idea of tying syntax and data types so completely. This lead to the invention of tie to allow objects to masquerade as other data types. (You can also achieve the same effect using overload, but tie is the more common approach in Perl.)
Another common mistake, made by many languages, is to start off by offering dynamic scoping rather than lexical. It is hard to revert this design decision later, and leads to long-lasting warts. The classic description of those warts in Perl is http://perl.plover.com/FAQs/Namespaces.html. Note that this was written before Perl added
our variables and
People legitimately disagree on static versus dynamic typing. I personally like dynamic typing. However it is important to have enough structure to let typos to be caught. Perl 5 does a good job of this with strict. But Perl 1-4 got this wrong. Several other languages have lint checkers that do the same thing as strict. As long as you are good about enforcing lint checking, that is acceptable.
If you're looking for more bad ideas (lots of them), learn PHP and study its history. My favorite past mistake (long ago fixed because it lead to so many security holes) was defaulting to allowing anyone to set any variable by passing in form parameters. But that is far from the only mistake.